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234,136 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Chemical ID(s) = YCP

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Search Summary

This query matches 30 Structures.

Refinements

Structure Determination Methodology

experimental (30)

Scientific Name of Source Organism

	Homo sapiens (14)
	synthetic construct (13)
	Staphylococcus aureus subsp. aureus NCTC 8325 (4)
	Streptomyces pristinaespiralis (3)
	Bacillus subtilis (2)
	Bacillus subtilis subsp. subtilis str. 168 (2)
	Bos taurus (1)
	Mesorhizobium japonicum MAFF 303099 (1)
	Mycobacterium tuberculosis (1)
	Neisseria meningitidis (1)

More...

Taxonomy

	Eukaryota (16)
	Bacteria (14)
	other sequences (13)

Experimental Method

	X-RAY DIFFRACTION (25)
	ELECTRON MICROSCOPY (5)

Polymer Entity Type

Protein (30)

Refinement Resolution (Å)

	1.0 - 1.5 (4)
	1.5 - 2.0 (9)
	2.0 - 2.5 (6)
	2.5 - 3.0 (6)
	3.0 - 3.5 (4)
	3.5 - 4.0 (1)

Release Date

	1995 - 1999 (1)
	2005 - 2009 (2)
	2010 - 2014 (4)
	2015 - 2019 (10)
	2020 - 2024 (13)

Enzyme Classification Name

	Hydrolases (14)
	Isomerases (7)
	Lyases (3)
	Oxidoreductases (2)
	Translocases (1)

Membrane Protein Annotation

	mpstruc (5)
	PDBTM (4)
	MemProtMD (3)
	OPM (1)

Symmetry Type

	Asymmetric (15)
	Cyclic (9)
	Dihedral (7)

SCOP Classification

	Alpha and beta proteins (a/b) (5)
	All beta proteins (7)
	All alpha proteins (1)
	Alpha and beta proteins (a+b) (4)
	Artifacts (1)

AllSelected

1 to 25 of 30 Structures

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1EFR \| pdb_00001efr	Download File View File

BOVINE MITOCHONDRIAL F1-ATPASE COMPLEXED WITH THE PEPTIDE ANTIBIOTIC EFRAPEPTIN

Abrahams, J.P., Buchanan, S.K., Van Raaij, M.J., Fearnley, I.M., Leslie, A.G.W., Walker, J.E.

(1996) Proc Natl Acad Sci U S A 93: 9420

Released	1997-02-12
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Bos taurus Tolypocladium inflatum
Macromolecule	BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT ALPHA (protein) BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT BETA (protein) BOVINE MITOCHONDRIAL F1-ATPASE SUBUNIT GAMMA (protein) EFRAPEPTIN C (protein)
Unique Ligands	ADP, ANP, MG

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2ITK \| pdb_00002itk	Download File View File

human Pin1 bound to D-PEPTIDE

Noel, J.P., Zhang, Y.

(2007) ACS Chem Biol 2: 320-328

Released	2007-05-22
Method	X-RAY DIFFRACTION 1.45 Å
Organisms	Homo sapiens
Macromolecule	D-Peptide (protein) Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (protein)
Unique Ligands	PE4

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2Q5A \| pdb_00002q5a	Download File View File

human Pin1 bound to L-PEPTIDE

Noel, J.P., Zhang, Y.

(2007) ACS Chem Biol 2: 320-328

Released	2007-06-26
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens
Macromolecule	Five residue peptide (protein) Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (protein)
Unique Ligands	16P

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2XDW \| pdb_00002xdw	Download File View File

Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide

Racys, D.T., Rea, D., Fulop, V., Wills, M.

(2010) Bioorg Med Chem 18: 4775

Released	2010-06-23
Method	X-RAY DIFFRACTION 1.35 Å
Organisms	Sus scrofa synthetic construct
Macromolecule	Prolyl endopeptidase (protein) SYNTHETIC PEPTIDE PHQ-PRO-YCP (protein)
Unique Ligands	GOL, TAM

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3KTJ \| pdb_00003ktj	Download File View File

Structure of ClpP in complex with ADEP2 in monoclinic crystal form

Lee, B.-G., Brotz-Oesterhelt, H., Song, H.K.

(2010) Nat Struct Mol Biol 17: 471-478

Released	2010-03-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus subtilis
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) Acyldepsipeptide 2 (protein)
Unique Ligands	NHE

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3KTK \| pdb_00003ktk	Download File View File

Structure of ClpP in complex with ADEP2 in triclinic crystal form

Lee, B.-G., Brotz-Oesterhelt, H., Song, H.K.

(2010) Nat Struct Mol Biol 17: 471-478

Released	2010-03-23
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Bacillus subtilis
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) Acyldepsipeptide 2 (protein)

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4P7X \| pdb_00004p7x	Download File View File

L-pipecolic acid-bound L-proline cis-4-hydroxylase

Shomura, Y., Koketsu, K., Moriwaki, K., Hayashi, M., Mitsuhashi, S., Hara, R., Kino, K., Higuchi, Y.

(2015) ACS Synth Biol 4: 383-392

Released	2014-09-17
Method	X-RAY DIFFRACTION 1.3 Å
Organisms	Mesorhizobium japonicum MAFF 303099
Macromolecule	L-proline cis-4-hydroxylase (protein)
Unique Ligands	AKG, CO, CXS, SO4, YCP

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5GZI \| pdb_00005gzi	Download File View File

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published

Released	2018-01-17
Method	X-RAY DIFFRACTION 2.17 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NAD, YCP

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5GZM \| pdb_00005gzm	Download File View File

Cyclodeaminase_PA

Ying, H., Chen, K.

To be published

Released	2018-01-17
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NAD, YCP

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5USP \| pdb_00005usp	Download File View File

Insulin with proline analog Pip at position B28 in the T2 state

Lieblich, S.A., Fang, K.Y., Tirrell, D.A.

To be published

Released	2018-02-21
Method	X-RAY DIFFRACTION 1.174 Å
Organisms	Homo sapiens
Macromolecule	Insulin Chain A (protein) Insulin Chain B (protein)
Unique Ligands	NA

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5USS \| pdb_00005uss	Download File View File

Insulin with proline analog PiP at position B28 in the R6 state

Lieblich, S.A., Fang, K.Y., Tirrell, D.A.

To be published

Released	2018-02-21
Method	X-RAY DIFFRACTION 2.061 Å
Organisms	Homo sapiens
Macromolecule	Insulin Chain A (protein) Insulin Chain B (protein)
Unique Ligands	CL, IPH, ZN

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5VZ2 \| pdb_00005vz2	Download File View File

Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide

Griffith, E.C., Lee, R.E.

(2019) ACS Infect Dis

Released	2017-06-21
Method	X-RAY DIFFRACTION 2.26 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325 synthetic construct
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) Acyldepsipeptide (protein)

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5W18 \| pdb_00005w18	Download File View File

Staphylococcus aureus ClpP in complex with (S)-N-((2R,6S,8aS,14aS,20S,23aS)-2,6-dimethyl-5,8,14,19,23-pentaoxooctadecahydro-1H,5H,14H,19H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1]oxa[4,7,10,13]tetraazacyclohexadecin-20-yl)-3-phenyl-2-(3-phenylureido)propanamide

Lee, R.E., Griffith, E.C.

(2019) ACS Infect Dis

Released	2017-08-09
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325 synthetic construct
Macromolecule	9V7-PHE-SER-PRO-YCP-ALA-MP8 (protein) ATP-dependent Clp protease proteolytic subunit (protein)

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5YU1 \| pdb_00005yu1	Download File View File

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Min, K.J., Yoon, H.J., Matsuura, A., Kim, Y.H., Lee, H.H.

(2018) Mol Cells 41: 331-341

Released	2018-05-02
Method	X-RAY DIFFRACTION 1.923 Å
Organisms	Streptomyces pristinaespiralis
Macromolecule	Lysine cyclodeaminase (protein)
Unique Ligands	NA, NAD, YCP

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6NAH \| pdb_00006nah	Download File View File

Crystal structure of Neisseria meningitidis ClpP protease in complex with Acyldepsipeptide-14 (ADEP-14)

Mabanglo, M.F., Houry, W.A.

(2019) Commun Biol 2: 410-410

Released	2019-11-13
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Neisseria meningitidis synthetic construct
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) Acyldepsipeptide-14 (protein)
Unique Ligands	OCA

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6O33 \| pdb_00006o33	Download File View File

Crystal Structure Analysis of PIN1

Seo, H.-S., Dhe-Paganon, S.

To be published

Released	2020-02-26
Method	X-RAY DIFFRACTION 1.74 Å
Organisms	Homo sapiens
Macromolecule	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (protein) peptide (protein)
Unique Ligands	SO4

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6O34 \| pdb_00006o34	Download File View File

Crystal Structure Analysis of PIN1

Seo, H.-S., Dhe-Paganon, S.

To be published

Released	2020-02-26
Method	X-RAY DIFFRACTION 1.57 Å
Organisms	Homo sapiens
Macromolecule	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (protein) peptide (protein)
Unique Ligands	2PE, GOL, SO4

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6PKA \| pdb_00006pka	Download File View File

Structure of ClpP from Staphylococcus aureus in complex with ureadepsipeptide

Griffith, E.C., Lee, R.E.

(2019) ACS Infect Dis 5: 1915-1925

Released	2019-11-06
Method	X-RAY DIFFRACTION 2.25 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325 synthetic construct
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide (protein)

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6PMD \| pdb_00006pmd	Download File View File

Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide

Griffith, E.C., Lee, R.E.

(2019) ACS Infect Dis 5: 1915-1925

Released	2019-11-06
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Staphylococcus aureus subsp. aureus NCTC 8325 synthetic construct
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide (protein)
Unique Ligands	MPD

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6VGN \| pdb_00006vgn	Download File View File

ClpP1P2 complex from M. tuberculosis bound to ADEP

Ripstein, Z.A., Vahidi, S., Rubinstein, J.L., Kay, L.E.

(2020) Proc Natl Acad Sci U S A 117: 5895-5906

Released	2020-03-18
Method	ELECTRON MICROSCOPY 3.1 Å
Organisms	Mycobacterium tuberculosis synthetic construct
Macromolecule	ATP-dependent Clp protease proteolytic subunit (protein) ATP-dependent Clp protease proteolytic subunit 1 (protein) R0M-WFP-ALO-PRO-YCP-ALA-MP8 (protein)

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7P80 \| pdb_00007p80	Download File View File

Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compressed state)

Lee, B.-G., Kim, L., Kim, M.K., Kwon, D.H., Song, H.K.

(2022) EMBO J 41: e109755-e109755

Released	2022-06-29
Method	X-RAY DIFFRACTION 2.98 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 synthetic construct
Macromolecule	ADEP2 (protein) ATP-dependent Clp protease proteolytic subunit (protein)

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7P81 \| pdb_00007p81	Download File View File

Crystal structure of ClpP from Bacillus subtilis in complex with ADEP2 (compact state)

Lee, B.-G., Kim, L., Kim, M.K., Kwon, D.H., Song, H.K.

(2022) EMBO J 41: e109755-e109755

Released	2022-06-29
Method	X-RAY DIFFRACTION 2.79 Å
Organisms	Bacillus subtilis subsp. subtilis str. 168 synthetic construct
Macromolecule	ADEP2 (protein) ATP-dependent Clp protease proteolytic subunit (protein)

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8DNY \| pdb_00008dny	Download File View File

Cryo-EM structure of the human Sec61 complex inhibited by decatransin

Park, E., Itskanov, S.

(2023) Nat Chem Biol 19: 1063-1071

Released	2023-05-24
Method	ELECTRON MICROSCOPY 2.85 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Decatransin peptide inhibitor (protein) Protein transport protein Sec61 subunit alpha isoform 1 (protein) Protein transport protein Sec61 subunit beta (protein) Protein transport protein Sec61 subunit gamma (protein)

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8P2Z \| pdb_00008p2z	Download File View File

Structure of human SIT1 bound to L-pipecolate (focussed map / refinement)

Li, H.Z., Pike, A.C.W., Chi, G., Hansen, J.S., Lee, S.G., Rodstrom, K.E.J., Bushell, S.R., Speedman, D., Evans, A., Wang, D., He, D., Shrestha, L., Nasrallah, C., Chalk, R., Moreira, T., MacLean, E.M., Marsden, B., Bountra, C., Burgess-Brown, N.A., Dafforn, T.R., Carpenter, E.P., Sauer, D.B.

(2024) Nat Commun 15: 5503-5503

Released	2024-06-12
Method	ELECTRON MICROSCOPY 3.5 Å
Organisms	Homo sapiens
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Sodium- and chloride-dependent transporter XTRP3 (protein)
Unique Ligands	CL, NAG, YCP

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8P30 \| pdb_00008p30	Download File View File

Structure of human SIT1:ACE2 complex (open PD conformation) bound to L-pipecolate

(2024) Nat Commun 15: 5503-5503

Released	2024-06-12
Method	ELECTRON MICROSCOPY 3.29 Å
Organisms	Homo sapiens
Macromolecule	Processed angiotensin-converting enzyme 2 (protein) Sodium- and chloride-dependent transporter XTRP3 (protein)
Unique Ligands	CL, NAG, NDG, YCP, ZN
Unique branched monosaccharides	BMA, MAN, NAG

1 to 25 of 30 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1EFR | pdb_00001efr

2ITK | pdb_00002itk

2Q5A | pdb_00002q5a

2XDW | pdb_00002xdw

3KTJ | pdb_00003ktj

3KTK | pdb_00003ktk

4P7X | pdb_00004p7x

5GZI | pdb_00005gzi

5GZM | pdb_00005gzm

5USP | pdb_00005usp

5USS | pdb_00005uss

5VZ2 | pdb_00005vz2

5W18 | pdb_00005w18

5YU1 | pdb_00005yu1

6NAH | pdb_00006nah

6O33 | pdb_00006o33

6O34 | pdb_00006o34

6PKA | pdb_00006pka

6PMD | pdb_00006pmd

6VGN | pdb_00006vgn

7P80 | pdb_00007p80

7P81 | pdb_00007p81

8DNY | pdb_00008dny

8P2Z | pdb_00008p2z

8P30 | pdb_00008p30