5DGV

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog

PDB DOI: https://doi.org/10.2210/pdb5DGV/pdb
NAKB: 5DGV

Classification: RIBOSOME
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2015-08-28 Released: 2016-12-14
Deposition Author(s): Melnikov, S., Mailliot, J., Shin, B.-S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.
Funding Organization(s): French National Research Agency, Austrian Science Fund, European Research Council, Human Frontier Science Program, Russian Government Program of Competitive Growh of Kazan Federal University, Intramural Research Program of the National Institutes of Health

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.284
R-Value Work: 0.238
R-Value Observed: 0.239

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

Melnikov, S., Mailliot, J., Shin, B.-S., Rigger, L., Yusupova, G., Micura, R., Dever, T.E., Yusupov, M.

To be published.

Macromolecule Content

Total Structure Weight: 6,271.24 kDa
Atom Count: 402,683
Modelled Residue Count: 33,345
Deposited Residue Count: 35,334
Unique protein chains: 80
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S0-A	B [auth S0], CC [auth s0]	251	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32905 Go to UniProtKB: P32905
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UniProt Group	P32905
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S1-A	C [auth S1], DC [auth s1]	254	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P33442 Go to UniProtKB: P33442
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UniProt Group	P33442
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	D [auth S2], EC [auth s2]	253	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25443 Go to UniProtKB: P25443
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UniProt Group	P25443
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3	E [auth S3], FC [auth s3]	239	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05750 Go to UniProtKB: P05750
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UniProt Group	P05750
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4-A	F [auth S4], GC [auth s4]	260	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX35 Go to UniProtKB: P0CX35
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UniProt Group	P0CX35
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	G [auth S5], HC [auth s5]	224	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26783 Go to UniProtKB: P26783
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UniProt Group	P26783
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6-A	H [auth S6], IC [auth s6]	236	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX37 Go to UniProtKB: P0CX37
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UniProt Group	P0CX37
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7-A	I [auth S7], JC [auth s7]	189	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26786 Go to UniProtKB: P26786
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UniProt Group	P26786
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8-A	J [auth S8], KC [auth s8]	200	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX39 Go to UniProtKB: P0CX39
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UniProt Group	P0CX39
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9-A	K [auth S9], LC [auth s9]	196	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore O13516 Go to UniProtKB: O13516
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UniProt Group	O13516
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S10-A	L [auth C0], MC [auth c0]	105	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08745 Go to UniProtKB: Q08745
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UniProt Group	Q08745
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11-A	M [auth C1], NC [auth c1]	155	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX47 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX47 Go to UniProtKB: P0CX47
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UniProt Group	P0CX47
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S12	N [auth C2], OC [auth c2]	142	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P48589 Go to UniProtKB: P48589
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UniProt Group	P48589
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	O [auth C3], PC [auth c3]	150	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05756 Go to UniProtKB: P05756
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UniProt Group	P05756
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14-A	P [auth C4], QC [auth c4]	136	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06367 Go to UniProtKB: P06367
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UniProt Group	P06367
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15	Q [auth C5], RC [auth c5]	141	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q01855 Go to UniProtKB: Q01855
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UniProt Group	Q01855
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16-A	R [auth C6], SC [auth c6]	142	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX51 Go to UniProtKB: P0CX51
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UniProt Group	P0CX51
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17-A	S [auth C7], TC [auth c7]	136	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02407 Go to UniProtKB: P02407
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UniProt Group	P02407
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18-A	T [auth C8], UC [auth c8]	145	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX55 Go to UniProtKB: P0CX55
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UniProt Group	P0CX55
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19-A	U [auth C9], VC [auth c9]	143	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07280 Go to UniProtKB: P07280
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UniProt Group	P07280
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S20	V [auth D0], WC [auth d0]	120	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38701 Go to UniProtKB: P38701
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UniProt Group	P38701
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21-A	W [auth D1], XC [auth d1]	87	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C0V8 Go to UniProtKB: P0C0V8
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UniProt Group	P0C0V8
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S22-A	X [auth D2], YC [auth d2]	129	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C0W1 Go to UniProtKB: P0C0W1
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UniProt Group	P0C0W1
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23-A	Y [auth D3], ZC [auth d3]	144	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX29 Go to UniProtKB: P0CX29
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UniProt Group	P0CX29
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S24-A	AD [auth d4], Z [auth D4]	134	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX31 Go to UniProtKB: P0CX31
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UniProt Group	P0CX31
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25-A	AA [auth D5], BD [auth d5]	107	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E792 Go to UniProtKB: Q3E792
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UniProt Group	Q3E792
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S26-B	BA [auth D6], CD [auth d6]	97	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39939 Go to UniProtKB: P39939
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UniProt Group	P39939
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27-A	CA [auth D7], DD [auth d7]	81	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35997 Go to UniProtKB: P35997
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28-A	DA [auth D8], ED [auth d8]	66	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E7X9 Go to UniProtKB: Q3E7X9
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UniProt Group	Q3E7X9
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S29-A	EA [auth D9], FD [auth d9]	55	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41057 Go to UniProtKB: P41057
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UniProt Group	P41057
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S30-A	FA [auth E0]	60	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX33 Go to UniProtKB: P0CX33
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UniProt Group	P0CX33
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S31	GA [auth E1], HD [auth e1]	76	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05759 Go to UniProtKB: P05759
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UniProt Group	P05759
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein subunit beta-like protein	HA [auth SR], ID [auth sR]	318	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38011 Go to UniProtKB: P38011
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UniProt Group	P38011
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Suppressor protein STM1	IA [auth SM], JD [auth sM]	263	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2-A	MA [auth L2], ND [auth l2]	253	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX45 Go to UniProtKB: P0CX45
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UniProt Group	P0CX45
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	NA [auth L3], OD [auth l3]	386	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14126 Go to UniProtKB: P14126
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UniProt Group	P14126
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4-A	OA [auth L4], PD [auth l4]	361	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10664 Go to UniProtKB: P10664
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UniProt Group	P10664
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	PA [auth L5], QD [auth l5]	296	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26321 Go to UniProtKB: P26321
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UniProt Group	P26321
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6-A	QA [auth L6], RD [auth l6]	175	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02326 Go to UniProtKB: Q02326
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UniProt Group	Q02326
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-A	RA [auth L7], SD [auth l7]	243	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05737 Go to UniProtKB: P05737
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UniProt Group	P05737
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8-A (eL8)	SA [auth L8], TD [auth l8]	255	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9-A	TA [auth L9], UD [auth l9]	191	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05738 Go to UniProtKB: P05738
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UniProt Group	P05738
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	UA [auth M0], VD [auth m0]	220	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41805 Go to UniProtKB: P41805
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UniProt Group	P41805
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11-B	VA [auth M1], WD [auth m1]	173	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q3E757 Go to UniProtKB: Q3E757
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UniProt Group	Q3E757
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13-A	WA [auth M3], YD [auth m3]	198	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12690 Go to UniProtKB: Q12690
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UniProt Group	Q12690
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-A	XA [auth M4], ZD [auth m4]	137	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L15-A	AE [auth m5], YA [auth M5]	203	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L16-A	BE [auth m6], ZA [auth M6]	198	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P26784
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17-A	AB [auth M7], CE [auth m7]	183	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P05740
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18-A	BB [auth M8], DE [auth m8]	185	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0CX49
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19-A	CB [auth M9], EE [auth m9]	188	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0CX82
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L20-A	DB [auth N0], FE [auth n0]	172	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX23 Go to UniProtKB: P0CX23
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UniProt Group	P0CX23
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21-A	EB [auth N1], GE [auth n1]	159	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02753 Go to UniProtKB: Q02753
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UniProt Group	Q02753
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22-A	FB [auth N2], HE [auth n2]	120	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P05749
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23-A	GB [auth N3], IE [auth n3]	136	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0CX41
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24-A	HB [auth N4], JE [auth n4]	155	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P04449
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L25	IB [auth N5], KE [auth n5]	141	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P04456
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-A	JB [auth N6], LE [auth n6]	126	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P05743
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27-A	KB [auth N7], ME [auth n7]	135	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H6 Go to UniProtKB: P0C2H6
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UniProt Group	P0C2H6
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	LB [auth N8], NE [auth n8]	148	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P02406
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	MB [auth N9], OE [auth n9]	58	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05747 Go to UniProtKB: P05747
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UniProt Group	P05747
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	NB [auth O0], PE [auth o0]	104	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14120 Go to UniProtKB: P14120
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UniProt Group	P14120
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31-A	OB [auth O1], QE [auth o1]	112	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0C2H8
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	PB [auth O2], RE [auth o2]	129	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38061 Go to UniProtKB: P38061
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UniProt Group	P38061
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L33-A	QB [auth O3], SE [auth o3]	106	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P05744
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34-A	RB [auth O4], TE [auth o4]	119	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P87262 Go to UniProtKB: P87262
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UniProt Group	P87262
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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35-A	SB [auth O5], UE [auth o5]	119	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0CX84
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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36-A	TB [auth O6], VE [auth o6]	99	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P05745
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Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37-A	UB [auth O7], WE [auth o7]	87	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49166 Go to UniProtKB: P49166
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UniProt Group	P49166
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Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	VB [auth O8], XE [auth o8]	77	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P49167
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Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	WB [auth O9], YE [auth o9]	50	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P04650
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Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-60S ribosomal protein L40	XB [auth Q0], ZE [auth q0]	52	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CH08 Go to UniProtKB: P0CH08
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UniProt Group	P0CH08
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Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L41-A	AF [auth q1], YB [auth Q1]	25	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX86 Go to UniProtKB: P0CX86
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UniProt Group	P0CX86
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Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L42-A	BF [auth q2], ZB [auth Q2]	105	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX27 Go to UniProtKB: P0CX27
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UniProt Group	P0CX27
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Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L43-A	AC [auth Q3], CF [auth q3]	91	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0CX25
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Entity ID: 80
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S30-A	GD [auth e0]	62	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P0CX33
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Entity ID: 81
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L12-A (uL11)	XD [auth m2]	160	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 82
Molecule	Chains	Sequence Length	Organism	Details	Image
60S acidic ribosomal protein P0	DF [auth p0]	311	Saccharomyces cerevisiae S288C	Mutation(s): 0
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UniProt Group	P05317
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Entity ID: 83
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein P1 alpha/P2 beta	EF [auth p1]	47	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 84
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein P1 alpha/P2 beta	FF [auth p2]	46	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Entity ID: 1
Molecule	Chains	Length	Organism	Image
Saccharomyces cerevisiae S288c RDN37-1 miscRNA	A [auth 2], BC [auth 6]	1,800	Saccharomyces cerevisiae S288C
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Entity ID: 36
Molecule	Chains	Length	Organism	Image
25S ribosomal RNA	JA [auth 1], KD [auth 5]	3,396	Saccharomyces cerevisiae S288C
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Entity ID: 37
Molecule	Chains	Length	Organism	Image
5S ribosomal RNA	KA [auth 3], LD [auth 7]	121	Saccharomyces cerevisiae S288C
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Entity ID: 38
Molecule	Chains	Length	Organism	Image
5.8S ribosomal RNA	LA [auth 4], MD [auth 8]	158	Saccharomyces cerevisiae S288C
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Entity ID: 85
Molecule	Chains	Length	Organism	Image
DNA (5'-R(CPCP(8AN)(Pro)*(Pro))-3')	GF [auth C], HF [auth D]	5	Saccharomyces cerevisiae S288C
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPS Query on SPS Download Ideal Coordinates CCD File SDF format, chain AG [auth D] SDF format, chain YF [auth C] MOL2 format, chain AG [auth D] MOL2 format, chain YF [auth C] mmCIF format, chain AG [auth D] mmCIF format, chain YF [auth C]	AG [auth D], YF [auth C]	SPARSOMYCIN C₁₃ H₁₉ N₃ O₅ S₂ XKLZIVIOZDNKEQ-CLQLPEFOSA-N		Interactions Focus chain AG [auth D] Focus chain YF [auth C] Interactions & Density Focus chain AG [auth D] Focus chain YF [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain IF [auth D6] SDF format, chain JF [auth D7] SDF format, chain KF [auth D9] SDF format, chain LF [auth E1] SDF format, chain MF [auth O7] SDF format, chain NF [auth Q0] SDF format, chain OF [auth Q2] SDF format, chain PF [auth Q3] SDF format, chain QF [auth d6] SDF format, chain SF [auth d9] SDF format, chain UF [auth o7] SDF format, chain WF [auth q2] SDF format, chain XF [auth q3] SDF format, chain RF [auth d7] SDF format, chain TF [auth e1] SDF format, chain VF [auth q0] MOL2 format, chain IF [auth D6] MOL2 format, chain JF [auth D7] MOL2 format, chain KF [auth D9] MOL2 format, chain LF [auth E1] MOL2 format, chain MF [auth O7] MOL2 format, chain NF [auth Q0] MOL2 format, chain OF [auth Q2] MOL2 format, chain PF [auth Q3] MOL2 format, chain QF [auth d6] MOL2 format, chain SF [auth d9] MOL2 format, chain UF [auth o7] MOL2 format, chain WF [auth q2] MOL2 format, chain XF [auth q3] MOL2 format, chain RF [auth d7] MOL2 format, chain TF [auth e1] MOL2 format, chain VF [auth q0] mmCIF format, chain IF [auth D6] mmCIF format, chain JF [auth D7] mmCIF format, chain KF [auth D9] mmCIF format, chain LF [auth E1] mmCIF format, chain MF [auth O7] mmCIF format, chain NF [auth Q0] mmCIF format, chain OF [auth Q2] mmCIF format, chain PF [auth Q3] mmCIF format, chain QF [auth d6] mmCIF format, chain SF [auth d9] mmCIF format, chain UF [auth o7] mmCIF format, chain WF [auth q2] mmCIF format, chain XF [auth q3] mmCIF format, chain RF [auth d7] mmCIF format, chain TF [auth e1] mmCIF format, chain VF [auth q0]	IF [auth D6] JF [auth D7] KF [auth D9] LF [auth E1] MF [auth O7] IF [auth D6], JF [auth D7], KF [auth D9], LF [auth E1], MF [auth O7], NF [auth Q0], OF [auth Q2], PF [auth Q3], QF [auth d6], RF [auth d7], SF [auth d9], TF [auth e1], UF [auth o7], VF [auth q0], WF [auth q2], XF [auth q3]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IF [auth D6] Focus chain JF [auth D7] Focus chain KF [auth D9] Focus chain LF [auth E1] Focus chain MF [auth O7] Focus chain NF [auth Q0] Focus chain OF [auth Q2] Focus chain PF [auth Q3] Focus chain QF [auth d6] Focus chain RF [auth d7] Focus chain SF [auth d9] Focus chain TF [auth e1] Focus chain UF [auth o7] Focus chain VF [auth q0] Focus chain WF [auth q2] Focus chain XF [auth q3] Interactions & Density Focus chain IF [auth D6] Focus chain JF [auth D7] Focus chain KF [auth D9] Focus chain LF [auth E1] Focus chain MF [auth O7] Focus chain NF [auth Q0] Focus chain OF [auth Q2] Focus chain PF [auth Q3] Focus chain QF [auth d6] Focus chain RF [auth d7] Focus chain SF [auth d9] Focus chain TF [auth e1] Focus chain UF [auth o7] Focus chain VF [auth q0] Focus chain WF [auth q2] Focus chain XF [auth q3]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BG [auth D] SDF format, chain ZF [auth C] MOL2 format, chain BG [auth D] MOL2 format, chain ZF [auth C] mmCIF format, chain BG [auth D] mmCIF format, chain ZF [auth C]	BG [auth D], ZF [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BG [auth D] Focus chain ZF [auth C] Interactions & Density Focus chain BG [auth D] Focus chain ZF [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.284
R-Value Work: 0.238
R-Value Observed: 0.239
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 437.14	α = 90
b = 287.91	β = 98.76
c = 303.85	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-12-14

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	--
French National Research Agency	France	ANR-11-BSV8-006 01
Austrian Science Fund	Austria	P21641
Austrian Science Fund	Austria	I1040
European Research Council		294312
Human Frontier Science Program		RGP0062
Human Frontier Science Program		RGP2012
Russian Government Program of Competitive Growh of Kazan Federal University	Russian Federation	--
Intramural Research Program of the National Institutes of Health	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-12-14
Type: Initial release
Version 1.1: 2017-03-22
Changes: Derived calculations
Version 1.2: 2024-01-10
Changes: Advisory, Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

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5DGV

Complex of yeast 80S ribosome with hypusine-containing/non-modified eIF5A and/or a peptidyl-tRNA analog

Coping with proline stalling: structural basis of hypusine-induced protein synthesis by the eukaryotic ribosome

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