SMTL ID : 1q3k.1

Crystal structure of creatinine amidohydrolase (creatininase)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: E.33, D.44, H.119 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.33, A:D.44, A:H.119, H2O.1, H2O.1 ZN.2: 5 residues within 4Å: Chain A: H.35, D.44, H.177, E.182 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.35, A:D.44, A:E.182, A:E.182, H2O.1 ZN.4: 4 residues within 4Å: Chain B: E.33, D.44, H.119 Ligands: ZN.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.33, B:D.44, B:H.119, H2O.5, H2O.5 ZN.5: 5 residues within 4Å: Chain B: H.35, D.44, H.177, E.182 Ligands: ZN.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.35, B:D.44, B:E.182, H2O.5, H2O.5 ZN.7: 4 residues within 4Å: Chain C: E.33, D.44, H.119 Ligands: ZN.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.33, C:D.44, C:H.119, H2O.10, H2O.10 ZN.8: 6 residues within 4Å: Chain C: E.33, H.35, D.44, H.177, E.182 Ligands: ZN.7 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.35, C:D.44, C:E.182, H2O.10, H2O.10 ZN.10: 4 residues within 4Å: Chain D: E.33, D.44, H.119 Ligands: ZN.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.33, D:D.44, D:H.119, H2O.14, H2O.14 ZN.11: 5 residues within 4Å: Chain D: H.35, D.44, H.177, E.182 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.35, D:D.44, D:E.182, D:E.182, H2O.14 ZN.12: 5 residues within 4Å: Chain E: E.33, D.44, H.119, E.121 Ligands: ZN.13 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.33, E:D.44, E:H.119, H2O.18, H2O.19 ZN.13: 6 residues within 4Å: Chain E: H.35, V.43, D.44, H.177, E.182 Ligands: ZN.12 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.35, E:D.44, E:E.182, H2O.18, H2O.18 ZN.15: 4 residues within 4Å: Chain F: E.33, D.44, H.119 Ligands: ZN.16 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.33, F:D.44, F:H.119, H2O.23, H2O.23 ZN.16: 5 residues within 4Å: Chain F: H.35, D.44, H.177, E.182 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.35, F:D.44, F:E.182, H2O.23, H2O.23

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: L.67, Q.68, Y.69 Chain B: L.67, Q.68, Y.69, T.97 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.68, B:Y.69, B:Y.69, A:Q.68, A:Y.69, A:Y.69 GOL.6: 8 residues within 4Å: Chain B: V.18, G.21, D.22, C.23, G.109, V.110, R.111, R.112 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.21, B:G.21, B:D.22, B:C.23, B:R.111, B:R.112 Water bridges: B:G.109 GOL.9: 7 residues within 4Å: Chain C: L.67, Q.68, Y.69 Chain D: L.67, Q.68, Y.69, T.97 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.68, C:Y.69, D:Q.68, D:Y.69, D:Y.69 GOL.14: 7 residues within 4Å: Chain E: L.67, Q.68, Y.69 Chain F: L.67, Q.68, Y.69, T.97 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.68, E:Y.69, E:Y.69, F:Q.68, F:Y.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beuth, B. et al., Crystal structure of creatininase from Pseudomonas putida: A novel fold and a case of convergent evolution. J.Mol.Biol. (2003)

Release Date

2003-08-12

Peptides

creatininase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

creatininase