SMTL ID : 3dug.1

Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-octamer

Ligands

32 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.64, H.66, K.184, D.317 Ligands: ZN.4, ARG.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.64, A:H.66, A:D.317, A:D.317 ZN.2: 3 residues within 4Å: Chain A: H.306, G.337, E.342 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.306, A:E.342, A:E.342 ZN.3: 3 residues within 4Å: Chain A: T.130, D.370, E.394 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.130, A:E.394 ZN.4: 6 residues within 4Å: Chain A: H.144, K.184, H.225, H.245 Ligands: ZN.1, ARG.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.225, A:H.245 ZN.7: 6 residues within 4Å: Chain B: H.64, H.66, K.184, D.317 Ligands: ZN.10, ARG.11 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.64, B:H.66, B:D.317, B:D.317 ZN.8: 2 residues within 4Å: Chain B: H.306, E.342 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.306, B:E.342, B:E.342 ZN.9: 2 residues within 4Å: Chain B: T.130, E.394 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.130, B:E.394 ZN.10: 6 residues within 4Å: Chain B: H.144, K.184, H.225, H.245 Ligands: ZN.7, ARG.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.225, B:H.245 ZN.16: 6 residues within 4Å: Chain C: H.64, H.66, K.184, D.317 Ligands: ZN.19, ARG.20 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.64, C:H.66, C:D.317, C:D.317 ZN.17: 3 residues within 4Å: Chain C: H.306, G.337, E.342 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.306, C:E.342, C:E.342, H2O.4 ZN.18: 2 residues within 4Å: Chain C: T.130, E.394 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.130, C:E.394 ZN.19: 6 residues within 4Å: Chain C: H.144, K.184, H.225, H.245 Ligands: ZN.16, ARG.20 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.225, C:H.245 ZN.21: 6 residues within 4Å: Chain D: H.64, H.66, K.184, D.317 Ligands: ZN.24, ARG.25 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.64, D:H.66, D:D.317, D:D.317 ZN.22: 3 residues within 4Å: Chain D: H.306, G.337, E.342 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.306, D:E.342, D:E.342, H2O.5 ZN.23: 3 residues within 4Å: Chain D: T.130, D.370, E.394 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.130, D:E.394 ZN.24: 6 residues within 4Å: Chain D: H.144, K.184, H.225, H.245 Ligands: ZN.21, ARG.25 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.225, D:H.245 ZN.27: 6 residues within 4Å: Chain E: H.64, H.66, K.184, D.317 Ligands: ZN.30, ARG.31 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.64, E:H.66, E:D.317, E:D.317 ZN.28: 3 residues within 4Å: Chain E: H.306, G.337, E.342 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.306, E:E.342, E:E.342 ZN.29: 2 residues within 4Å: Chain E: T.130, E.394 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.130, E:E.394 ZN.30: 6 residues within 4Å: Chain E: H.144, K.184, H.225, H.245 Ligands: ZN.27, ARG.31 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.225, E:H.245 ZN.34: 6 residues within 4Å: Chain F: H.64, H.66, K.184, D.317 Ligands: ZN.37, ARG.38 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.64, F:H.66, F:D.317, F:D.317 ZN.35: 2 residues within 4Å: Chain F: H.306, E.342 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.306, F:E.342, F:E.342 ZN.36: 3 residues within 4Å: Chain F: T.130, D.370, E.394 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.130, F:E.394 ZN.37: 6 residues within 4Å: Chain F: H.144, K.184, H.225, H.245 Ligands: ZN.34, ARG.38 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.225, F:H.245 ZN.39: 6 residues within 4Å: Chain G: H.64, H.66, K.184, D.317 Ligands: ZN.42, ARG.43 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.64, G:H.66, G:D.317, G:D.317 ZN.40: 3 residues within 4Å: Chain G: H.306, G.337, E.342 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.306, G:E.342, G:E.342 ZN.41: 5 residues within 4Å: Chain G: T.102, T.103, T.130, D.370, E.394 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:T.130, G:E.394, H2O.8 ZN.42: 6 residues within 4Å: Chain G: H.144, K.184, H.225, H.245 Ligands: ZN.39, ARG.43 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:H.225, G:H.245 ZN.45: 6 residues within 4Å: Chain H: H.64, H.66, K.184, D.317 Ligands: ZN.48, ARG.49 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.64, H:H.66, H:D.317, H:D.317 ZN.46: 3 residues within 4Å: Chain H: H.306, G.337, E.342 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.306, H:E.342, H:E.342, H2O.11 ZN.47: 3 residues within 4Å: Chain H: T.130, D.370, E.394 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:T.130, H:E.394, H2O.11 ZN.48: 6 residues within 4Å: Chain H: H.144, K.184, H.225, H.245 Ligands: ZN.45, ARG.49 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:H.225, H:H.245

8 x ARG: ARGININE(Non-covalent)

ARG.5: 16 residues within 4Å: Chain A: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, E.291, V.294, Q.298, D.317, I.320 Ligands: ZN.1, ZN.4 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:I.320 Hydrogen bonds: A:V.191, A:M.192, A:D.267, A:D.317, R.5, R.5 Salt bridges: A:H.144, A:H.225, A:H.227, A:H.245, A:D.267, A:E.291 ARG.11: 18 residues within 4Å: Chain B: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, S.271, I.274, E.291, V.294, Q.298, D.317, I.320 Ligands: ZN.7, ZN.10 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:I.320 Hydrogen bonds: B:V.191, B:M.192, B:Q.298, B:Q.298, B:Q.298, B:D.317 Salt bridges: B:H.144, B:H.225, B:H.227, B:H.245, B:D.267, B:E.291 ARG.20: 15 residues within 4Å: Chain C: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, E.291, Q.298, D.317, I.320 Ligands: ZN.16, ZN.19 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:V.270, C:I.320 Hydrogen bonds: C:V.191, C:M.192, C:D.267, C:Q.298, C:D.317 Salt bridges: C:H.144, C:H.225, C:H.227, C:H.245, C:D.267, C:E.291 ARG.25: 18 residues within 4Å: Chain D: H.144, K.184, 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 Ligands: ZN.21, ZN.24 13 PLIP interactions: 13 interactions with chain D, Hydrophobic interactions: D:V.191, D:I.320 Hydrogen bonds: D:V.191, D:M.192, D:Q.298, D:Q.298, D:D.317 Salt bridges: D:H.144, D:H.225, D:H.227, D:H.245, D:D.267, D:E.291 ARG.31: 18 residues within 4Å: Chain E: H.144, K.184, 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 Ligands: ZN.27, ZN.30 16 PLIP interactions: 14 interactions with chain E, 2 Ligand-Ligand interactions Hydrophobic interactions: E:V.191, E:I.320 Hydrogen bonds: E:V.191, E:M.192, E:H.245, E:Q.298, E:Q.298, E:D.317 Salt bridges: E:H.144, E:H.225, E:H.227, E:H.245, E:D.267, E:E.291 Water bridges: R.31, R.31 ARG.38: 19 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, I.274, E.291, V.294, G.295, Q.298, D.317, I.320 Ligands: ZN.34, ZN.37 14 PLIP interactions: 14 interactions with chain F, Hydrophobic interactions: 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 Salt bridges: F:H.144, F:H.225, F:H.227, F:H.245, F:D.267, F:E.291 ARG.43: 19 residues within 4Å: Chain G: H.144, G.190, V.191, M.192, H.225, H.227, H.245, D.267, V.270, S.271, I.274, E.291, V.294, G.295, Q.298, D.317, I.320 Ligands: ZN.39, ZN.42 13 PLIP interactions: 13 interactions with chain G, Hydrophobic interactions: G:I.320 Hydrogen bonds: G:V.191, G:M.192, G:Q.298, G:Q.298, G:Q.298, G:D.317 Salt bridges: G:H.144, G:H.225, G:H.227, G:H.245, G:D.267, G:E.291 ARG.49: 17 residues within 4Å: Chain H: 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 Ligands: ZN.45, ZN.48 11 PLIP interactions: 11 interactions with chain H, Hydrophobic interactions: H:I.320 Hydrogen bonds: H:V.191, H:M.192, 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

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: H.66, G.69, N.70, D.71, N.92, G.319, H.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.66, A:N.70, A:D.71 GOL.12: 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 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.82, A:H.83, B:S.82, B:S.82 GOL.13: 7 residues within 4Å: Chain B: H.66, G.69, N.70, D.71, N.92, G.319, H.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.66, B:N.70 GOL.14: 7 residues within 4Å: Chain B: D.71, W.88, N.92, K.95, F.321, D.322, H.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.321, B:H.323 GOL.15: 5 residues within 4Å: Chain B: H.216, G.219, M.220, K.221, D.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.216, B:D.241 GOL.26: 4 residues within 4Å: Chain D: D.119, E.122, R.123 Chain G: E.76 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.122, D:R.123 Water bridges: D:R.118, D:R.118 GOL.32: 7 residues within 4Å: Chain E: H.66, G.69, N.70, D.71, N.92, G.319, H.323 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:I.67, E:N.70, E:D.71 GOL.33: 7 residues within 4Å: Chain E: S.82, H.83, N.111 Chain F: S.82, H.83, N.111 Chain G: E.153 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:S.82, E:S.82, E:H.83, E:N.111 GOL.44: 7 residues within 4Å: Chain G: H.66, G.69, N.70, D.71, N.92, G.319, H.323 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:H.66, G:D.71 GOL.50: 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 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain C Hydrogen bonds: H:S.82, H:S.82, H:H.83, C:S.82

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

2008-08-05

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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