5J7L

Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracycline

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

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This is version 3.0 of the entry. See complete history. 


Literature

Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors.

Cocozaki, A.I., Altman, R.B., Huang, J., Buurman, E.T., Kazmirski, S.L., Doig, P., Prince, D.B., Blanchard, S.C., Cate, J.H., Ferguson, A.D.

(2016) Proc Natl Acad Sci U S A 113: 8188-8193

  • DOI: https://doi.org/10.1073/pnas.1605127113
  • Primary Citation of Related Structures:  
    5IT8, 5J5B, 5J7L, 5J88, 5J8A, 5J91, 5JC9

  • PubMed Abstract: 

    Mutations conferring resistance to translation inhibitors often alter the structure of rRNA. Reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents. The translation inhibitors negamycin and tetracycline interfere with tRNA binding to the aminoacyl-tRNA site on the small 30S ribosomal subunit. However, two negamycin resistance mutations display unexpected differential antibiotic susceptibility profiles. Mutant U1060A in 16S Escherichia coli rRNA is resistant to both antibiotics, whereas mutant U1052G is simultaneously resistant to negamycin and hypersusceptible to tetracycline. Using a combination of microbiological, biochemical, single-molecule fluorescence transfer experiments, and X-ray crystallography, we define the specific structural defects in the U1052G mutant 70S E. coli ribosome that explain its divergent negamycin and tetracycline susceptibility profiles. Unexpectedly, the U1052G mutant ribosome possesses a second tetracycline binding site that correlates with its hypersusceptibility. The creation of a previously unidentified antibiotic binding site raises the prospect of identifying similar phenomena in antibiotic-resistant pathogens in the future.

    • Organizational Affiliation: 

    Structure and Biophysics, Discovery Sciences, AstraZeneca Pharmaceuticals, Waltham, MA 02451;


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
CA [auth BB]		224Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
DA [auth BC]		206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
EA [auth BD]		205Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
FA [auth BE]		155Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
GA [auth BF]		106Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
HA [auth BG]		151Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
IA [auth BH]		129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI],
JA [auth BI]		127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ],
KA [auth BJ]		99Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
LA [auth BK]		117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL],
MA [auth BL]		123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM],
NA [auth BM]		114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN],
OA [auth BN]		100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO],
PA [auth BO]		88Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
QA [auth BP]		82Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ],
RA [auth BQ]		80Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR],
SA [auth BR]		55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS],
TA [auth BS]		79Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT],
UA [auth BT]		86Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth AU],
VA [auth BU]		56Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32V [auth C1],
WA [auth D1]		56Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33W [auth C2],
XA [auth D2]		51Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth C3],
YA [auth D3]		46Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35Y [auth C4],
ZA [auth D4]		64Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36AB [auth D5],
Z [auth C5]		38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth C0],
BB [auth D0]		58Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2DB [auth CC],
GB [auth DC]		271Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3EB [auth CD],
HB [auth DD]		209Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4DC [auth DE],
IB [auth CE]		201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5EC [auth DF],
JB [auth CF]		177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FC [auth DG],
KB [auth CG]		176Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9GC [auth DH],
LB [auth CH]		149Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11HC [auth DJ],
MB [auth CJ]		134Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IC [auth DK],
NB [auth CK]		142Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JC [auth DL],
OB [auth CL]		123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KC [auth DM],
PB [auth CM]		144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LC [auth DN],
QB [auth CN]		136Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MC [auth DO],
RB [auth CO]		125Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NC [auth DP],
SB [auth CP]		117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OC [auth DQ],
TB [auth CQ]		114Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PC [auth DR],
UB [auth CR]		117Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QC [auth DS],
VB [auth CS]		103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RC [auth DT],
WB [auth CT]		110Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SC [auth DU],
XB [auth CU]		93Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TC [auth DV],
YB [auth CV]		102Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UC [auth DW],
ZB [auth CW]		94Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AC [auth CX],
VC [auth DX]		76Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BC [auth CY],
WC [auth DY]		77Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CC [auth CZ],
XC [auth DZ]		62Escherichia coli K-12Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10YC [auth DI]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth AA],
BA		1,534Escherichia coli K-12
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Entity ID: 28
MoleculeChains LengthOrganismImage
5S rRNACB,
ZC [auth DB]		120Escherichia coli K-12
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Entity ID: 31
MoleculeChains LengthOrganismImage
23S rRNAFB [auth CA]2,904Escherichia coli K-12
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Entity ID: 54
MoleculeChains LengthOrganismImage
23S rRNAAD [auth DA]2,904Escherichia coli K-12
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TAC
Query on TAC
Download Ideal Coordinates CCD File 
CG [auth AA],
DG [auth AA],
XH [auth BA],
YH [auth BA]		TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
1PE
Query on 1PE
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KX [auth DA],
TW [auth DA]		PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4
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AP [auth DS]
BX [auth DA]
SF [auth AA]
VO [auth DQ]
WH [auth BA]
AP [auth DS],
BX [auth DA],
SF [auth AA],
VO [auth DQ],
WH [auth BA],
XO [auth DR],
YX [auth DA]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
GUN
Query on GUN
Download Ideal Coordinates CCD File 
TX [auth DA]GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
PGE
Query on PGE
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EI [auth D1]
EP [auth DU]
HY [auth DA]
LX [auth DA]
RP [auth DA]
EI [auth D1],
EP [auth DU],
HY [auth DA],
LX [auth DA],
RP [auth DA],
UW [auth DA],
WX [auth DA],
ZO [auth DS],
ZX [auth DA]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SPD
Query on SPD
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GY [auth DA],
OX [auth DA],
RW [auth DA],
VW [auth DA]		SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
TRS
Query on TRS
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CY [auth DA]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD
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AX [auth DA]
BP [auth DS]
CP [auth DT]
DP [auth DT]
MO [auth DE]
AX [auth DA],
BP [auth DS],
CP [auth DT],
DP [auth DT],
MO [auth DE],
MX [auth DA],
NO [auth DE],
OO [auth DK],
PX [auth DA],
SO [auth DN],
SX [auth DA],
TF [auth AA],
YF [auth AA],
YW [auth DA]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG
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AY [auth DA]
FG [auth AL]
FI [auth D1]
GI [auth D3]
HX [auth DA]
AY [auth DA],
FG [auth AL],
FI [auth D1],
GI [auth D3],
HX [auth DA],
IX [auth DA],
IY [auth DA],
JY [auth DA],
PO [auth DL],
TO [auth DP],
UO [auth DQ]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PUT
Query on PUT
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BY [auth DA]
DX [auth DA]
DY [auth DA]
EY [auth DA]
FY [auth DA]
BY [auth DA],
DX [auth DA],
DY [auth DA],
EY [auth DA],
FY [auth DA],
NX [auth DA],
QO [auth DM],
SW [auth DA],
UF [auth AA],
UX [auth DA],
VF [auth AA],
VX [auth DA],
WF [auth AA],
WW [auth DA],
XF [auth AA],
XW [auth DA]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN
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EG [auth AB],
GG [auth C5],
HI [auth D5]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO
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CX [auth DA]
DI [auth D1]
FP [auth DB]
FX [auth DA]
GX [auth DA]
CX [auth DA],
DI [auth D1],
FP [auth DB],
FX [auth DA],
GX [auth DA],
PP [auth DB],
QP [auth DB],
QX [auth DA],
RX [auth DA],
SP [auth DA],
TP [auth DA],
XX [auth DA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY
Query on ACY
Download Ideal Coordinates CCD File 
EX [auth DA],
JX [auth DA],
ZW [auth DA]		ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG
Query on MG
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AE [auth AA]
AF [auth AA]
AG [auth AA]
AH [auth BA]
AI [auth BA]
AE [auth AA],
AF [auth AA],
AG [auth AA],
AH [auth BA],
AI [auth BA],
AJ [auth CA],
AK [auth CA],
AL [auth CA],
AM [auth CA],
AN [auth CA],
AO [auth CA],
AQ [auth DA],
AR [auth DA],
AS [auth DA],
AT [auth DA],
AU [auth DA],
AV [auth DA],
AW [auth DA],
BD [auth AA],
BE [auth AA],
BF [auth AA],
BG [auth AA],
BH [auth BA],
BI [auth BA],
BJ [auth CA],
BK [auth CA],
BL [auth CA],
BM [auth CA],
BN [auth CA],
BO [auth CA],
BQ [auth DA],
BR [auth DA],
BS [auth DA],
BT [auth DA],
BU [auth DA],
BV [auth DA],
BW [auth DA],
CD [auth AA],
CE [auth AA],
CF [auth AA],
CH [auth BA],
CI [auth BA],
CJ [auth CA],
CK [auth CA],
CL [auth CA],
CM [auth CA],
CN [auth CA],
CO [auth CA],
CQ [auth DA],
CR [auth DA],
CS [auth DA],
CT [auth DA],
CU [auth DA],
CV [auth DA],
CW [auth DA],
DD [auth AA],
DE [auth AA],
DF [auth AA],
DH [auth BA],
DJ [auth CA],
DK [auth CA],
DL [auth CA],
DM [auth CA],
DN [auth CA],
DO [auth CA],
DQ [auth DA],
DR [auth DA],
DS [auth DA],
DT [auth DA],
DU [auth DA],
DV [auth DA],
DW [auth DA],
ED [auth AA],
EE [auth AA],
EF [auth AA],
EH [auth BA],
EJ [auth CA],
EK [auth CA],
EL [auth CA],
EM [auth CA],
EN [auth CA],
EO [auth CA],
EQ [auth DA],
ER [auth DA],
ES [auth DA],
ET [auth DA],
EU [auth DA],
EV [auth DA],
EW [auth DA],
FD [auth AA],
FE [auth AA],
FF [auth AA],
FH [auth BA],
FJ [auth CA],
FK [auth CA],
FL [auth CA],
FM [auth CA],
FN [auth CA],
FO [auth CA],
FQ [auth DA],
FR [auth DA],
FS [auth DA],
FT [auth DA],
FU [auth DA],
FV [auth DA],
FW [auth DA],
GD [auth AA],
GE [auth AA],
GF [auth AA],
GH [auth BA],
GJ [auth CA],
GK [auth CA],
GL [auth CA],
GM [auth CA],
GN [auth CA],
GO [auth CA],
GP [auth DB],
GQ [auth DA],
GR [auth DA],
GS [auth DA],
GT [auth DA],
GU [auth DA],
GV [auth DA],
GW [auth DA],
HD [auth AA],
HE [auth AA],
HF [auth AA],
HG [auth BA],
HH [auth BA],
HJ [auth CA],
HK [auth CA],
HL [auth CA],
HM [auth CA],
HN [auth CA],
HO [auth CA],
HP [auth DB],
HQ [auth DA],
HR [auth DA],
HS [auth DA],
HT [auth DA],
HU [auth DA],
HV [auth DA],
HW [auth DA],
ID [auth AA],
IE [auth AA],
IF [auth AA],
IG [auth BA],
IH [auth BA],
II [auth CB],
IJ [auth CA],
IK [auth CA],
IL [auth CA],
IM [auth CA],
IN [auth CA],
IO [auth CA],
IP [auth DB],
IQ [auth DA],
IR [auth DA],
IS [auth DA],
IT [auth DA],
IU [auth DA],
IV [auth DA],
IW [auth DA],
JD [auth AA],
JE [auth AA],
JF [auth AA],
JG [auth BA],
JH [auth BA],
JI [auth CB],
JJ [auth CA],
JK [auth CA],
JL [auth CA],
JM [auth CA],
JN [auth CA],
JO [auth CA],
JP [auth DB],
JQ [auth DA],
JR [auth DA],
JS [auth DA],
JT [auth DA],
JU [auth DA],
JV [auth DA],
JW [auth DA],
KD [auth AA],
KE [auth AA],
KF [auth AA],
KG [auth BA],
KH [auth BA],
KI [auth CB],
KJ [auth CA],
KK [auth CA],
KL [auth CA],
KM [auth CA],
KN [auth CA],
KO [auth CA],
KP [auth DB],
KQ [auth DA],
KR [auth DA],
KS [auth DA],
KT [auth DA],
KU [auth DA],
KV [auth DA],
KW [auth DA],
KY [auth DA],
LD [auth AA],
LE [auth AA],
LF [auth AA],
LG [auth BA],
LH [auth BA],
LI [auth CA],
LJ [auth CA],
LK [auth CA],
LL [auth CA],
LM [auth CA],
LN [auth CA],
LO [auth DD],
LP [auth DB],
LQ [auth DA],
LR [auth DA],
LS [auth DA],
LT [auth DA],
LU [auth DA],
LV [auth DA],
LW [auth DA],
LY [auth DA],
MD [auth AA],
ME [auth AA],
MF [auth AA],
MG [auth BA],
MH [auth BA],
MI [auth CA],
MJ [auth CA],
MK [auth CA],
ML [auth CA],
MM [auth CA],
MN [auth CA],
MP [auth DB],
MQ [auth DA],
MR [auth DA],
MS [auth DA],
MT [auth DA],
MU [auth DA],
MV [auth DA],
MW [auth DA],
MY [auth DA],
ND [auth AA],
NE [auth AA],
NF [auth AA],
NG [auth BA],
NH [auth BA],
NI [auth CA],
NJ [auth CA],
NK [auth CA],
NL [auth CA],
NM [auth CA],
NN [auth CA],
NP [auth DB],
NQ [auth DA],
NR [auth DA],
NS [auth DA],
NT [auth DA],
NU [auth DA],
NV [auth DA],
NW [auth DA],
NY [auth DA],
OD [auth AA],
OE [auth AA],
OF [auth AA],
OG [auth BA],
OH [auth BA],
OI [auth CA],
OJ [auth CA],
OK [auth CA],
OL [auth CA],
OM [auth CA],
ON [auth CA],
OP [auth DB],
OQ [auth DA],
OR [auth DA],
OS [auth DA],
OT [auth DA],
OU [auth DA],
OV [auth DA],
OW [auth DA],
PD [auth AA],
PE [auth AA],
PF [auth AA],
PG [auth BA],
PH [auth BA],
PI [auth CA],
PJ [auth CA],
PK [auth CA],
PL [auth CA],
PM [auth CA],
PN [auth CA],
PQ [auth DA],
PR [auth DA],
PS [auth DA],
PT [auth DA],
PU [auth DA],
PV [auth DA],
PW [auth DA],
QD [auth AA],
QE [auth AA],
QF [auth AA],
QG [auth BA],
QH [auth BA],
QI [auth CA],
QJ [auth CA],
QK [auth CA],
QL [auth CA],
QM [auth CA],
QN [auth CA],
QQ [auth DA],
QR [auth DA],
QS [auth DA],
QT [auth DA],
QU [auth DA],
QV [auth DA],
QW [auth DA],
RD [auth AA],
RE [auth AA],
RF [auth AA],
RG [auth BA],
RH [auth BA],
RI [auth CA],
RJ [auth CA],
RK [auth CA],
RL [auth CA],
RM [auth CA],
RN [auth CA],
RO [auth DM],
RQ [auth DA],
RR [auth DA],
RS [auth DA],
RT [auth DA],
RU [auth DA],
RV [auth DA],
SD [auth AA],
SE [auth AA],
SG [auth BA],
SH [auth BA],
SI [auth CA],
SJ [auth CA],
SK [auth CA],
SL [auth CA],
SM [auth CA],
SN [auth CA],
SQ [auth DA],
SR [auth DA],
SS [auth DA],
ST [auth DA],
SU [auth DA],
SV [auth DA],
TD [auth AA],
TE [auth AA],
TG [auth BA],
TH [auth BA],
TI [auth CA],
TJ [auth CA],
TK [auth CA],
TL [auth CA],
TM [auth CA],
TN [auth CA],
TQ [auth DA],
TR [auth DA],
TS [auth DA],
TT [auth DA],
TU [auth DA],
TV [auth DA],
UD [auth AA],
UE [auth AA],
UG [auth BA],
UH [auth BA],
UI [auth CA],
UJ [auth CA],
UK [auth CA],
UL [auth CA],
UM [auth CA],
UN [auth CA],
UP [auth DA],
UQ [auth DA],
UR [auth DA],
US [auth DA],
UT [auth DA],
UU [auth DA],
UV [auth DA],
VD [auth AA],
VE [auth AA],
VG [auth BA],
VH [auth BA],
VI [auth CA],
VJ [auth CA],
VK [auth CA],
VL [auth CA],
VM [auth CA],
VN [auth CA],
VP [auth DA],
VQ [auth DA],
VR [auth DA],
VS [auth DA],
VT [auth DA],
VU [auth DA],
VV [auth DA],
WD [auth AA],
WE [auth AA],
WG [auth BA],
WI [auth CA],
WJ [auth CA],
WK [auth CA],
WL [auth CA],
WM [auth CA],
WN [auth CA],
WO [auth DR],
WP [auth DA],
WQ [auth DA],
WR [auth DA],
WS [auth DA],
WT [auth DA],
WU [auth DA],
WV [auth DA],
XD [auth AA],
XE [auth AA],
XG [auth BA],
XI [auth CA],
XJ [auth CA],
XK [auth CA],
XL [auth CA],
XM [auth CA],
XN [auth CA],
XP [auth DA],
XQ [auth DA],
XR [auth DA],
XS [auth DA],
XT [auth DA],
XU [auth DA],
XV [auth DA],
YD [auth AA],
YE [auth AA],
YG [auth BA],
YI [auth CA],
YJ [auth CA],
YK [auth CA],
YL [auth CA],
YM [auth CA],
YN [auth CA],
YO [auth DR],
YP [auth DA],
YQ [auth DA],
YR [auth DA],
YS [auth DA],
YT [auth DA],
YU [auth DA],
YV [auth DA],
ZD [auth AA],
ZE [auth AA],
ZF [auth AA],
ZG [auth BA],
ZH [auth BA],
ZI [auth CA],
ZJ [auth CA],
ZK [auth CA],
ZL [auth CA],
ZM [auth CA],
ZN [auth CA],
ZP [auth DA],
ZQ [auth DA],
ZR [auth DA],
ZS [auth DA],
ZT [auth DA],
ZU [auth DA],
ZV [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T		L [auth AL],
MA [auth BL]		L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		EB [auth CD],
HB [auth DD]		L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		LC [auth DN],
QB [auth CN]		L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.41α = 90
b = 435.7β = 90
c = 625.25γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2017-05-31
    Changes: Structure summary
  • Version 2.0: 2018-08-01
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 3.0: 2018-08-15
    Changes: Atomic model, Data collection