SMTL ID : 3a6f.1

W174F mutant creatininase, Type II

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 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, CAC.3 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.4: 5 residues within 4Å: Chain B: E.34, D.45, H.120 Ligands: ZN.5, CAC.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.34, B:D.45, B:H.120, H2O.5 MN.7: 5 residues within 4Å: Chain C: E.34, D.45, H.120 Ligands: ZN.8, CAC.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.34, C:D.45, C:H.120, H2O.10 MN.10: 5 residues within 4Å: Chain D: E.34, D.45, H.120 Ligands: ZN.11, CAC.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.34, D:D.45, D:H.120, H2O.14 MN.13: 5 residues within 4Å: Chain E: E.34, D.45, H.120 Ligands: ZN.14, CAC.15 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.34, E:D.45, E:H.120, H2O.19 MN.16: 5 residues within 4Å: Chain F: E.34, D.45, H.120 Ligands: ZN.17, CAC.18 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.34, F:D.45, H2O.24

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.36, D.45, E.183 Ligands: MN.1, CAC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.36, A:D.45, A:E.183, A:E.183 ZN.5: 6 residues within 4Å: Chain B: H.36, D.45, H.178, E.183 Ligands: MN.4, CAC.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.36, B:D.45, B:E.183, B:E.183 ZN.8: 6 residues within 4Å: Chain C: H.36, D.45, H.178, E.183 Ligands: MN.7, CAC.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.36, C:D.45, C:E.183, C:E.183 ZN.11: 6 residues within 4Å: Chain D: H.36, D.45, H.178, E.183 Ligands: MN.10, CAC.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.36, D:D.45, D:E.183, D:E.183 ZN.14: 7 residues within 4Å: Chain E: H.36, V.44, D.45, H.178, E.183 Ligands: MN.13, CAC.15 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.36, E:D.45, E:E.183, E:E.183 ZN.17: 6 residues within 4Å: Chain F: H.36, D.45, H.178, E.183 Ligands: MN.16, CAC.18 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.36, F:D.45, F:E.183, F:E.183

6 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 13 residues within 4Å: Chain A: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, E.122, W.154, H.178, E.183 Ligands: MN.1, ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.121 CAC.6: 14 residues within 4Å: Chain B: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, E.122, W.154, E.177, H.178, E.183 Ligands: MN.4, ZN.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.121, B:H.178 CAC.9: 13 residues within 4Å: Chain C: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, E.122, W.154, H.178, E.183 Ligands: MN.7, ZN.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.121 CAC.12: 14 residues within 4Å: Chain D: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, E.122, W.154, E.177, H.178, E.183 Ligands: MN.10, ZN.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.121, D:H.178 CAC.15: 12 residues within 4Å: Chain E: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, W.154, H.178, E.183 Ligands: MN.13, ZN.14 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Y.121 CAC.18: 14 residues within 4Å: Chain F: E.34, H.36, D.45, S.78, G.119, H.120, Y.121, E.122, W.154, E.177, H.178, E.183 Ligands: MN.16, ZN.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.121, F:H.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, K. et al., Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase. J.Mol.Biol. (2010)

Release Date

2010-02-09

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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