SMTL ID : 1v7z.1

creatininase-product complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.34, D.45, H.120 Ligands: ZN.2, CRN.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.34, A:D.45, A:H.120, H2O.1 MN.7: 5 residues within 4Å: Chain B: E.34, D.45, H.120 Ligands: ZN.8, CRN.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.34, B:D.45, B:H.120, H2O.13 MN.13: 5 residues within 4Å: Chain C: E.34, D.45, H.120 Ligands: ZN.14, CRN.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.34, C:D.45, C:H.120, H2O.25 MN.19: 5 residues within 4Å: Chain D: E.34, D.45, H.120 Ligands: ZN.20, CRN.24 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.34, D:D.45, D:H.120, H2O.36 MN.25: 5 residues within 4Å: Chain E: E.34, D.45, H.120 Ligands: ZN.26, CRN.30 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.34, E:D.45, E:H.120, H2O.47 MN.31: 5 residues within 4Å: Chain F: E.34, D.45, H.120 Ligands: ZN.32, CRN.36 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.34, F:D.45, F:H.120, H2O.59

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.36, D.45, H.178, E.183 Ligands: MN.1, CRN.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.36, A:D.45, A:E.183, A:E.183 ZN.8: 6 residues within 4Å: Chain B: H.36, D.45, H.178, E.183 Ligands: MN.7, CRN.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.36, B:D.45, B:E.183, B:E.183 ZN.14: 6 residues within 4Å: Chain C: H.36, D.45, H.178, E.183 Ligands: MN.13, CRN.18 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.36, C:D.45, C:E.183, C:E.183 ZN.20: 6 residues within 4Å: Chain D: H.36, D.45, H.178, E.183 Ligands: MN.19, CRN.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.36, D:D.45, D:E.183, D:E.183 ZN.26: 6 residues within 4Å: Chain E: H.36, D.45, H.178, E.183 Ligands: MN.25, CRN.30 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.36, E:D.45, E:E.183, E:E.183 ZN.32: 6 residues within 4Å: Chain F: H.36, D.45, H.178, E.183 Ligands: MN.31, CRN.36 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.36, F:D.45, F:E.183, F:E.183

18 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: R.113, K.147, E.256, F.257, P.258 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: R.113, K.147, E.256, F.257, P.258 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain C: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain C: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: R.113, K.147, E.256, F.257, P.258 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain D: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain D: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain D: R.113, K.147, E.256, F.257, P.258 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain E: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain E: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain E: R.113, K.147, E.256, F.257, P.258 Ligand excluded by PLIP SO4.33: 4 residues within 4Å: Chain F: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain F: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain F: R.113, K.147, E.256, F.257, P.258 Ligand excluded by PLIP

6 x CRN: N-[(E)-AMINO(IMINO)METHYL]-N-METHYLGLYCINE(Non-covalent)

CRN.6: 15 residues within 4Å: Chain A: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: MN.1, ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.78, A:Y.121, A:W.174, A:H.178 Salt bridges: A:H.36, A:H.120, A:H.178, A:E.183 CRN.12: 15 residues within 4Å: Chain B: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: MN.7, ZN.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.78, B:Y.121, B:W.174 Salt bridges: B:H.36, B:H.120, B:H.178, B:E.183 pi-Cation interactions: B:W.154 CRN.18: 15 residues within 4Å: Chain C: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: MN.13, ZN.14 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.121, C:H.178 Salt bridges: C:H.36, C:H.120, C:H.178, C:E.183 pi-Cation interactions: C:W.154 CRN.24: 15 residues within 4Å: Chain D: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: MN.19, ZN.20 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.78, D:Y.121, D:W.174 Salt bridges: D:H.36, D:H.120, D:H.178, D:E.183 pi-Cation interactions: D:W.154 CRN.30: 15 residues within 4Å: Chain E: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: MN.25, ZN.26 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:S.78, E:Y.121, E:W.174, E:H.178 Salt bridges: E:H.36, E:H.120, E:H.178, E:E.183 pi-Cation interactions: E:W.154 CRN.36: 15 residues within 4Å: Chain F: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: MN.31, ZN.32 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:S.78, F:Y.121, F:W.174 Salt bridges: F:H.36, F:H.120, F:H.178, F:E.183 pi-Cation interactions: F:W.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshimoto, T. et al., Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism. J.Mol.Biol. (2004)

Release Date

2004-01-27

Peptides

creatinine amidohydrolase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

creatinine amidohydrolase

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