SMTL ID : 1j2u.1

Creatininase Zn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.36, D.45, H.178, E.183 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.36, A:D.45, A:E.183, A:E.183, H2O.1 ZN.2: 4 residues within 4Å: Chain A: E.34, D.45, H.120 Ligands: ZN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.34, A:D.45, A:H.120, H2O.1, H2O.1 ZN.5: 5 residues within 4Å: Chain B: H.36, D.45, H.178, E.183 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.36, B:D.45, B:E.183, B:E.183, H2O.10 ZN.6: 4 residues within 4Å: Chain B: E.34, D.45, H.120 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.34, B:D.45, B:H.120, H2O.10, H2O.10 ZN.9: 5 residues within 4Å: Chain C: H.36, D.45, H.178, E.183 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.36, C:D.45, C:E.183, C:E.183, H2O.19 ZN.10: 4 residues within 4Å: Chain C: E.34, D.45, H.120 Ligands: ZN.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.34, C:D.45, C:H.120, H2O.19, H2O.19 ZN.13: 5 residues within 4Å: Chain D: H.36, D.45, H.178, E.183 Ligands: ZN.14 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.36, D:D.45, D:E.183, D:E.183, H2O.27 ZN.14: 4 residues within 4Å: Chain D: E.34, D.45, H.120 Ligands: ZN.13 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.34, D:D.45, D:H.120, H2O.27, H2O.27 ZN.16: 5 residues within 4Å: Chain E: H.36, D.45, H.178, E.183 Ligands: ZN.17 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.36, E:D.45, E:E.183, E:E.183, H2O.35 ZN.17: 4 residues within 4Å: Chain E: E.34, D.45, H.120 Ligands: ZN.16 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.34, E:D.45, E:H.120, H2O.35, H2O.35 ZN.19: 5 residues within 4Å: Chain F: H.36, D.45, H.178, E.183 Ligands: ZN.20 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.36, F:D.45, F:E.183, F:E.183, H2O.42 ZN.20: 4 residues within 4Å: Chain F: E.34, D.45, H.120 Ligands: ZN.19 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.34, F:D.45, F:H.120, H2O.42, H2O.43

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

SO4.3: 4 residues within 4Å: Chain A: A.51, K.54, R.55, Y.191 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.191 Water bridges: A:R.55, A:Y.191 Salt bridges: A:K.54, A:R.55 SO4.4: 4 residues within 4Å: Chain A: R.113, K.147, E.256, F.257 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.113, A:K.147 SO4.7: 4 residues within 4Å: Chain B: A.51, K.54, R.55, Y.191 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Y.191, B:Y.191, B:Y.191 Salt bridges: B:K.54, B:R.55 SO4.8: 4 residues within 4Å: Chain B: R.113, K.147, E.256, F.257 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.147 Salt bridges: B:R.113, B:K.147 SO4.11: 4 residues within 4Å: Chain C: A.51, K.54, R.55, Y.191 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.191 Water bridges: C:Y.191, C:Y.191 Salt bridges: C:K.54, C:R.55 SO4.12: 4 residues within 4Å: Chain C: R.113, K.147, E.256, F.257 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.113, C:K.147 SO4.15: 3 residues within 4Å: Chain D: K.54, R.55, Y.191 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.191, D:Y.191 Salt bridges: D:K.54, D:R.55 SO4.18: 4 residues within 4Å: Chain E: A.51, K.54, R.55, Y.191 4 PLIP interactions: 4 interactions with chain E Water bridges: E:Y.191, E:Y.191 Salt bridges: E:K.54, E:R.55 SO4.21: 4 residues within 4Å: Chain F: A.51, K.54, R.55, Y.191 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.191, F:Y.191 Salt bridges: F:K.54, F:R.55 SO4.22: 5 residues within 4Å: Chain F: R.113, K.147, E.256, F.257, P.258 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.113, F:K.147

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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