SMTL ID : 1ovm.1

Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.435, L.460, N.462, G.464 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.435, A:G.464, H2O.46 MG.2: 5 residues within 4Å: Chain B: D.435, L.460, N.462, G.464 Ligands: TPP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.435, B:G.464, H2O.162 MG.3: 5 residues within 4Å: Chain C: D.435, L.460, N.462, G.464 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.435, C:G.464 MG.4: 5 residues within 4Å: Chain D: D.435, L.460, N.462, G.464 Ligands: TPP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.435, D:G.464

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.5: 23 residues within 4Å: Chain A: G.384, T.385, G.408, S.409, I.410, G.434, D.435, G.436, A.437, N.462, G.464, Y.465, T.466, V.467, E.468 Chain B: V.26, P.27, G.28, E.52, T.74, V.77, H.116 Ligands: MG.1 19 PLIP interactions: 1 interactions with chain B, 18 interactions with chain A Water bridges: B:H.115, A:T.385, A:S.386, A:D.435, A:D.435 Hydrophobic interactions: A:I.410, A:Y.465, A:V.467, A:E.468 Hydrogen bonds: A:T.385, A:G.408, A:I.410, A:G.434, A:G.436, A:A.437, A:N.462, A:N.462, A:T.466, A:V.467 TPP.6: 23 residues within 4Å: Chain A: V.26, P.27, G.28, E.52, T.74, V.77, H.116 Chain B: G.384, T.385, G.408, S.409, I.410, G.434, D.435, G.436, A.437, N.462, G.464, Y.465, T.466, V.467, E.468 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.410, B:Y.465, B:V.467, B:E.468, A:V.77 Hydrogen bonds: B:T.385, B:T.385, B:G.408, B:I.410, B:G.434, B:D.435, B:G.436, B:A.437, B:N.462, B:N.462, B:T.466, B:V.467 Water bridges: B:T.385, B:S.386, B:S.386, A:E.52 TPP.7: 23 residues within 4Å: Chain C: G.384, T.385, G.408, S.409, I.410, G.434, D.435, G.436, A.437, N.462, G.464, Y.465, T.466, V.467, E.468 Chain D: V.26, P.27, G.28, E.52, T.74, V.77, H.116 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.410, C:Y.465 Hydrogen bonds: C:T.385, C:T.385, C:G.408, C:I.410, C:G.434, C:D.435, C:G.436, C:A.437, C:N.462, C:T.466, C:V.467 TPP.8: 24 residues within 4Å: Chain C: V.26, P.27, G.28, E.52, T.74, V.77, H.116 Chain D: G.384, T.385, G.408, S.409, I.410, G.434, D.435, G.436, A.437, L.440, N.462, G.464, Y.465, T.466, V.467, E.468 Ligands: MG.4 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.410, D:L.440, D:Y.465, D:V.467, D:E.468 Hydrogen bonds: D:T.385, D:G.408, D:I.410, D:G.434, D:D.435, D:G.436, D:A.437, D:G.464, D:T.466, D:V.467 Water bridges: D:S.386, C:E.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schutz, A. et al., Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid. Eur.J.Biochem. (2003)

Release Date

2003-06-03

Peptides

Indole-3-pyruvate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Indole-3-pyruvate decarboxylase