SMTL ID : 3a6d.1

Creatininase complexed with 1-methylguanidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: E.34, D.45, H.120 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.34, A:D.45, A:H.120, H2O.7, H2O.8 MN.7: 4 residues within 4Å: Chain B: E.34, D.45, H.120 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.34, B:D.45, B:H.120, H2O.15, H2O.15 MN.13: 4 residues within 4Å: Chain C: E.34, D.45, H.120 Ligands: ZN.14 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.34, C:D.45, C:H.120, H2O.17, H2O.22 MN.19: 5 residues within 4Å: Chain D: E.34, D.45, H.120 Ligands: ZN.20, MGX.21 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.34, D:D.45, D:H.120, H2O.22, H2O.26 MN.25: 5 residues within 4Å: Chain E: E.34, D.45, H.120 Ligands: ZN.26, MGX.27 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.34, E:D.45, E:H.120, H2O.29, H2O.30 MN.31: 4 residues within 4Å: Chain F: E.34, D.45, H.120 Ligands: ZN.32 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.42

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.36, D.45, H.178, E.183 Ligands: MN.1 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.8 ZN.8: 5 residues within 4Å: Chain B: H.36, D.45, H.178, E.183 Ligands: MN.7 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.15 ZN.14: 5 residues within 4Å: Chain C: H.36, D.45, H.178, E.183 Ligands: MN.13 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.17 ZN.20: 5 residues within 4Å: Chain D: H.36, D.45, H.178, E.183 Ligands: MN.19 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.26 ZN.26: 5 residues within 4Å: Chain E: H.36, D.45, H.178, E.183 Ligands: MN.25 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.30 ZN.32: 5 residues within 4Å: Chain F: H.36, D.45, H.178, E.183 Ligands: MN.31 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

6 x MGX: 1-METHYLGUANIDINE(Non-covalent)

MGX.3: 7 residues within 4Å: Chain A: S.78, Y.121, W.154, W.174, D.175, E.177, H.178 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.78, A:W.174, A:E.177, A:H.178 Water bridges: A:Y.121, A:Y.121 Salt bridges: A:E.183 pi-Cation interactions: A:W.154 MGX.9: 7 residues within 4Å: Chain B: S.78, Y.121, W.154, W.174, D.175, E.177, H.178 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.78, B:W.174, B:E.177, B:H.178 Water bridges: B:Y.121, B:Y.121 Salt bridges: B:E.183 pi-Cation interactions: B:W.154 MGX.15: 6 residues within 4Å: Chain C: S.78, Y.121, W.174, D.175, E.177, H.178 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.78, C:W.174, C:H.178 Water bridges: C:Y.121, C:Y.121 Salt bridges: C:E.183 pi-Cation interactions: C:W.154 MGX.21: 7 residues within 4Å: Chain D: S.78, Y.121, W.154, W.174, D.175, H.178 Ligands: MN.19 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.78, D:W.174, D:H.178 Water bridges: D:Y.121, D:Y.121, D:Y.121 Salt bridges: D:E.183 MGX.27: 8 residues within 4Å: Chain E: S.78, Y.121, W.154, W.174, D.175, E.177, H.178 Ligands: MN.25 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.78, E:W.174, E:H.178 Water bridges: E:Y.121, E:Y.121, E:Y.121 Salt bridges: E:E.183 MGX.33: 7 residues within 4Å: Chain F: S.78, Y.121, W.154, W.174, D.175, E.177, H.178 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.78, F:W.174, F:E.177 Water bridges: F:Y.121 Salt bridges: F:E.183 pi-Cation interactions: F:W.154

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

SO4.4: 4 residues within 4Å: Chain A: R.113, K.147, E.256, F.257 Ligand excluded by PLIP SO4.5: 4 residues within 4Å: Chain A: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain B: R.113, K.147, E.256, F.257 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain B: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: R.59, Q.247, R.254 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain C: R.113, K.147, E.256, F.257 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain C: R.59, Q.247, R.254 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 SO4.24: 3 residues within 4Å: Chain D: 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 SO4.30: 4 residues within 4Å: Chain E: 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: 4 residues within 4Å: Chain F: R.113, K.147, E.256, F.257 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain F: A.51, K.54, R.55, Y.191 Ligand excluded by PLIP

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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