SMTL ID : 3a6j.1

E122Q mutant creatininase complexed with creatine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.36, D.45, E.183 Ligands: CRN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.36, A:D.45, A:E.183, A:E.183 ZN.6: 4 residues within 4Å: Chain B: H.36, D.45, E.183 Ligands: CRN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.36, B:D.45, B:E.183, B:E.183 ZN.10: 4 residues within 4Å: Chain C: H.36, D.45, E.183 Ligands: CRN.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.36, C:D.45, C:E.183, C:E.183 ZN.14: 4 residues within 4Å: Chain D: H.36, D.45, H.178, E.183 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.17 ZN.17: 4 residues within 4Å: Chain E: H.36, D.45, E.183 Ligands: CRN.18 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.36, E:D.45, E:E.183, E:E.183 ZN.21: 4 residues within 4Å: Chain F: H.36, D.45, E.183 Ligands: CRN.22 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.36, F:D.45, F:E.183, F:E.183

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

CRN.2: 12 residues within 4Å: Chain A: E.34, H.36, D.45, S.78, H.120, Y.121, W.154, W.174, D.175, H.178, E.183 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.78, A:Y.121, A:W.174, A:H.178, A:H.178 Salt bridges: A:H.36, A:H.120, A:H.178, A:E.183 pi-Cation interactions: A:W.154 CRN.7: 12 residues within 4Å: Chain B: E.34, H.36, D.45, S.78, H.120, Y.121, W.174, D.175, E.177, H.178, E.183 Ligands: ZN.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.78, B:Y.121, B:W.174, B:E.177 Salt bridges: B:H.36, B:H.120, B:H.178, B:E.183 pi-Cation interactions: B:W.154 CRN.11: 13 residues within 4Å: Chain C: E.34, H.36, D.45, S.78, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: ZN.10 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:S.78, C:Y.121, C:W.174, C:E.177, C:H.178 Salt bridges: C:H.36, C:H.120, C:H.178, C:E.183 pi-Cation interactions: C:W.154 CRN.18: 12 residues within 4Å: Chain E: E.34, H.36, D.45, S.78, H.120, Y.121, W.154, W.174, D.175, H.178, E.183 Ligands: ZN.17 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:S.78, E:Y.121, E:W.174, E:H.178, E:H.178, E:E.183 Salt bridges: E:H.36, E:H.120, E:H.178, E:E.183 CRN.22: 13 residues within 4Å: Chain F: E.34, H.36, D.45, S.78, H.120, Y.121, W.154, W.174, D.175, E.177, H.178, E.183 Ligands: ZN.21 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:S.78, F:Y.121, F:W.174, F:E.177 Salt bridges: F:H.36, F:H.120, F:H.178, F:E.183 pi-Cation interactions: F:W.154

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

SO4.3: 5 residues within 4Å: Chain A: R.113, K.147, E.256, F.257, P.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.256 Salt bridges: A:R.113, A:K.147 SO4.4: 4 residues within 4Å: Chain A: A.51, K.54, R.55, Y.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.191, A:Y.191 Salt bridges: A:K.54, A:R.55 SO4.5: 3 residues within 4Å: Chain A: R.59, Q.247, R.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.247 Salt bridges: A:R.59, A:R.254 SO4.8: 4 residues within 4Å: Chain B: A.51, K.54, R.55, Y.191 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.191, B:Y.191 Salt bridges: B:K.54, B:R.55 SO4.9: 3 residues within 4Å: Chain B: R.59, Q.247, R.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.247, B:Q.247 Salt bridges: B:R.59, B:R.254 SO4.12: 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 SO4.13: 3 residues within 4Å: Chain C: R.59, Q.247, R.254 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.247, C:Q.247 Salt bridges: C:R.59, C:R.254 SO4.15: 3 residues within 4Å: Chain D: R.59, Q.247, R.254 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.247, D:Q.247 Salt bridges: D:R.59, D:R.254 SO4.16: 4 residues within 4Å: Chain D: A.51, 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 SO4.19: 3 residues within 4Å: Chain E: R.59, Q.247, R.254 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.247 Salt bridges: E:R.59, E:R.254 SO4.20: 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 SO4.23: 3 residues within 4Å: Chain F: R.59, Q.247, R.254 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Q.247, F:Q.247 Salt bridges: F:R.59, F:R.254 SO4.24: 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

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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