SMTL ID : 3be7.1

Crystal structure of Zn-dependent arginine carboxypeptidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x ARG: ARGININE(Non-covalent)

ARG.1: 16 residues within 4Å: Chain E: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, I.274, E.291, V.294, G.295, Q.298, D.317, I.320 15 PLIP interactions: 15 interactions with chain E, Hydrophobic interactions: E:V.191, E:I.320 Hydrogen bonds: E:H.144, E:V.191, E:M.192, E:Q.298, E:Q.298, E:Q.298 Water bridges: E:S.271 Salt bridges: E:H.144, E:H.225, E:H.227, E:H.245, E:D.267, E:E.291 ARG.4: 16 residues within 4Å: Chain B: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, I.274, E.291, V.294, G.295, Q.298, D.317, I.320 14 PLIP interactions: 13 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:I.320 Hydrogen bonds: B:V.191, B:M.192, B:Q.298, B:Q.298, B:D.317 Water bridges: B:S.271, R.4 Salt bridges: B:H.144, B:H.225, B:H.227, B:H.245, B:D.267, B:E.291 ARG.6: 15 residues within 4Å: Chain D: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, I.274, E.291, V.294, Q.298, D.317, I.320 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:I.320 Hydrogen bonds: D:V.191, D:M.192, D:Q.298, D:Q.298, D:D.317 Water bridges: D:H.225 Salt bridges: D:H.144, D:H.225, D:H.227, D:H.245, D:D.267, D:E.291 ARG.8: 15 residues within 4Å: Chain C: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, S.271, E.291, V.294, Q.298, D.317, I.320 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:I.320 Hydrogen bonds: C:V.191, C:M.192, C:Q.298, C:Q.298, C:Q.298, C:D.317 Water bridges: C:S.271 Salt bridges: C:H.144, C:H.225, C:H.227, C:H.245, C:D.267, C:E.291 ARG.11: 16 residues within 4Å: Chain F: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, S.271, E.291, V.294, G.295, Q.298, D.317, I.320 15 PLIP interactions: 14 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:V.191, F:I.320 Hydrogen bonds: F:V.191, F:M.192, F:Q.298, F:Q.298, F:Q.298, F:D.317 Water bridges: F:S.271, R.11 Salt bridges: F:H.144, F:H.225, F:H.227, F:D.267, F:E.291 ARG.15: 16 residues within 4Å: Chain G: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, I.274, E.291, V.294, G.295, Q.298, D.317, I.320 17 PLIP interactions: 17 interactions with chain G, Hydrophobic interactions: G:V.191, G:I.320 Hydrogen bonds: G:V.191, G:M.192, G:H.245, G:Q.298, G:Q.298, G:D.317 Water bridges: G:D.267, G:S.271, G:G.295 Salt bridges: G:H.144, G:H.225, G:H.227, G:H.245, G:D.267, G:E.291 ARG.19: 15 residues within 4Å: Chain H: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, I.274, E.291, V.294, Q.298, D.317, I.320 13 PLIP interactions: 13 interactions with chain H, Hydrophobic interactions: H:I.320 Hydrogen bonds: H:V.191, H:M.192, H:Q.298, H:Q.298, H:Q.298, H:D.317 Salt bridges: H:H.144, H:H.225, H:H.227, H:H.245, H:D.267, H:E.291 ARG.22: 15 residues within 4Å: Chain A: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, I.274, E.291, V.294, Q.298, D.317, I.320 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.320 Hydrogen bonds: A:H.144, A:V.191, A:M.192, A:H.245, A:Q.298, A:Q.298, A:Q.298 Water bridges: A:H.225, A:V.270, A:S.271 Salt bridges: A:H.144, A:H.225, A:H.227, A:H.245, A:D.267, A:E.291

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: H.66, I.67, G.69, N.70, D.71, N.92, G.319, H.323 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: S.82, H.83, N.111 Chain B: S.82, H.83, N.111 Chain C: E.153 Chain D: E.153 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain B: D.71, W.88, N.92, K.95, D.322, H.323 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain B: E.153 Chain C: S.82, H.83, N.111 Chain F: E.153 Chain H: S.82, H.83, N.111 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain D: H.66, V.68, G.69, N.70, D.71, N.92, G.319, H.323 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain D: D.119, E.122, R.123 Chain G: E.76 Ligand excluded by PLIP GOL.12: 9 residues within 4Å: Chain E: H.66, I.67, V.68, G.69, N.70, D.71, N.92, G.319, H.323 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain E: S.82, H.83, N.111 Chain F: S.82, H.83, N.111 Chain G: E.153 Chain H: E.153 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain F: I.121, E.122, G.124, K.393, E.394, K.396 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain F: D.71, W.88, N.92, K.95, F.321, D.322, H.323 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain F: H.216, G.219, M.220, K.221, D.241 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain G: H.66, I.67, G.69, N.70, D.71, N.92, G.319, H.323 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain H: H.216, G.239, V.240, D.241, N.260 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain H: A.109, A.110, P.136, A.137, C.145, S.158, E.159, G.160 Ligand excluded by PLIP GOL.25: 7 residues within 4Å: Chain H: D.71, W.88, N.92, K.95, F.321, D.322, H.323 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain H: H.66, I.67, V.68, G.69, N.70, D.71, N.92, G.319, H.323 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 2 residues within 4Å: Chain F: T.130, E.394 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.130, F:E.394, H2O.15, H2O.15, H2O.16 MG.21: 2 residues within 4Å: Chain H: T.130, E.394 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:E.394, H2O.19, H2O.21, H2O.22, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, D.F. et al., Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes. Biochemistry (2009)

Release Date

2007-11-27

Peptides

Zn-dependent arginine carboxypeptidase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Zn-dependent arginine carboxypeptidase

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