SMTL ID : 2vun.1

THE CRYSTAL STRUCTURE OF ENAMIDASE AT 1.9 A RESOLUTION - A NEW MEMBER OF THE AMIDOHYDROLASE SUPERFAMILY

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.67, H.69, E.164, D.276 Ligands: FE.2, CL.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.67, A:H.69, A:E.164, A:D.276, H2O.362 ZN.6: 6 residues within 4Å: Chain B: H.67, H.69, E.164, D.276 Ligands: FE.7, CL.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.67, B:H.69, B:E.164, B:D.276, H2O.677 ZN.10: 6 residues within 4Å: Chain C: H.67, H.69, E.164, D.276 Ligands: FE.11, CL.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.67, C:H.69, C:E.164, C:D.276, H2O.989 ZN.14: 6 residues within 4Å: Chain D: H.67, H.69, E.164, D.276 Ligands: FE.15, CL.16 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.67, D:H.69, D:E.164, D:D.276, H2O.1235

4 x FE: FE (III) ION(Non-covalent)

FE.2: 5 residues within 4Å: Chain A: E.164, H.193, H.220 Ligands: ZN.1, CL.3 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.164, A:H.193, A:H.220, H2O.205, H2O.222, H2O.362 FE.7: 5 residues within 4Å: Chain B: E.164, H.193, H.220 Ligands: ZN.6, CL.8 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.164, B:H.193, B:H.220, H2O.536, H2O.551, H2O.677 FE.11: 5 residues within 4Å: Chain C: E.164, H.193, H.220 Ligands: ZN.10, CL.12 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.164, C:H.193, C:H.220, H2O.854, H2O.863, H2O.989 FE.15: 5 residues within 4Å: Chain D: E.164, H.193, H.220 Ligands: ZN.14, CL.16 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.164, D:H.193, D:H.220, H2O.1128, H2O.1138, H2O.1235

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: H.69, D.276 Ligands: ZN.1, FE.2 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: H.69 Ligands: ZN.6, FE.7 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Ligands: ZN.10, FE.11 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain D: H.69, E.164, D.276 Ligands: ZN.14, FE.15 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: G.100, S.101, R.107, P.108, T.114, L.117, A.118, A.139, V.140, I.141 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.101, A:R.107, A:P.108, A:T.114, A:A.118, A:A.139, A:A.139, A:I.141 Water bridges: A:A.139 GOL.5: 5 residues within 4Å: Chain A: G.266, Q.267, L.268, G.269, R.270 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.267, A:G.269 Water bridges: A:G.266, A:Q.267, A:L.268, A:G.269 GOL.9: 10 residues within 4Å: Chain B: G.100, S.101, R.107, P.108, T.114, L.117, A.118, A.139, V.140, I.141 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.101, B:S.101, B:R.107, B:P.108, B:A.118, B:A.139, B:I.141 Water bridges: B:A.139 GOL.13: 10 residues within 4Å: Chain C: G.100, S.101, R.107, P.108, T.114, L.117, A.118, A.139, V.140, I.141 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.101, C:R.107, C:P.108, C:A.118, C:A.139, C:I.141 Water bridges: C:A.139 GOL.17: 10 residues within 4Å: Chain D: G.100, S.101, R.107, P.108, T.114, L.117, A.118, A.139, V.140, I.141 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:S.101, D:S.101, D:R.107, D:P.108, D:T.114, D:A.118, D:I.141 Water bridges: D:A.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kress, D. et al., The Crystal Structure of Enamidase: A Bifunctional Enzyme of the Nicotinate Catabolism. J.Mol.Biol. (2008)

Release Date

2008-12-09

Peptides

ENAMIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

ENAMIDASE