SMTL ID : 5euj.1 (5 other biounits)

PYRUVATE DECARBOXYLASE FROM ZYMOBACTER PALMAE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.435, N.462, G.464 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.435, A:G.464, H2O.3 MG.4: 4 residues within 4Å: Chain B: D.435, N.462, G.464 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.435, B:G.464, H2O.9 MG.6: 4 residues within 4Å: Chain C: D.435, N.462, G.464 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.435, C:G.464, H2O.15 MG.8: 4 residues within 4Å: Chain D: D.435, N.462, G.464 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.435, D:G.464, H2O.23

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 23 residues within 4Å: Chain A: T.383, G.384, D.385, G.408, H.409, I.410, G.434, D.435, G.436, S.437, L.440, N.462, G.464, Y.465, V.466, I.467, E.468 Chain B: A.24, G.25, E.49, V.74, H.113 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.410, A:L.440, A:Y.465, A:Y.465, A:I.467 Hydrogen bonds: A:D.385, A:G.408, A:I.410, A:G.434, A:G.436, A:S.437, A:N.462, A:V.466, A:I.467 Water bridges: A:S.386, A:D.435, A:D.435, A:S.437, A:S.437 TPP.5: 22 residues within 4Å: Chain A: A.24, G.25, E.49, V.74, H.113 Chain B: G.384, D.385, G.408, H.409, I.410, G.434, D.435, G.436, S.437, L.440, N.462, G.464, Y.465, V.466, I.467, E.468 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.410, B:L.440, B:Y.465, B:Y.465, B:I.467 Hydrogen bonds: B:D.385, B:G.408, B:I.410, B:G.434, B:G.436, B:S.437, B:N.462, B:V.466, B:I.467 Water bridges: B:S.386, B:D.435, B:D.435, B:S.437, B:S.437 TPP.7: 23 residues within 4Å: Chain C: T.383, G.384, D.385, G.408, H.409, I.410, G.434, D.435, G.436, S.437, L.440, N.462, G.464, Y.465, V.466, I.467, E.468 Chain D: A.24, G.25, E.49, V.74, H.113 Ligands: MG.6 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.410, C:L.440, C:Y.465, C:Y.465, C:I.467 Hydrogen bonds: C:D.385, C:G.408, C:I.410, C:G.434, C:G.436, C:S.437, C:N.462, C:N.462, C:V.466, C:I.467 Water bridges: C:S.386, C:D.435, C:S.437, C:S.437, D:E.49 TPP.9: 23 residues within 4Å: Chain C: A.24, G.25, E.49, V.74, H.113 Chain D: T.383, G.384, D.385, G.408, H.409, I.410, G.434, D.435, G.436, S.437, L.440, N.462, G.464, Y.465, V.466, I.467, E.468 Ligands: MG.8 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.410, D:L.440, D:Y.465, D:Y.465, D:I.467 Hydrogen bonds: D:D.385, D:G.408, D:I.410, D:G.434, D:G.436, D:S.437, D:N.462, D:V.466, D:I.467 Water bridges: D:S.386, D:D.435, D:S.437, D:N.462, C:E.49

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: S.217, A.244, N.287, M.405, Q.406 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.217, A:N.287 Water bridges: A:E.89, A:V.285, A:M.405

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buddrus, L. et al., Crystal structure of pyruvate decarboxylase from Zymobacter palmae. Acta Crystallogr.,Sect.F (2016)

Release Date

2016-09-14

Peptides

Pyruvate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate decarboxylase

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