SMTL ID : 1pvd.1

CRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE FROM THE YEAST SACCHAROMYCES CEREVISIAE AT 2.3 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.443, N.470, G.472 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.443, A:G.472, H2O.1 MG.3: 4 residues within 4Å: Chain B: D.443, N.470, G.472 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.443, B:G.472, H2O.10

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 20 residues within 4Å: Chain A: G.388, T.389, G.412, S.413, I.414, G.442, D.443, G.444, S.445, N.470, G.472, Y.473, T.474, I.475, E.476 Chain B: P.25, G.26, E.50, V.75 Ligands: MG.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.414, A:I.414, A:Y.473, A:Y.473 Hydrogen bonds: A:T.389, A:G.412, A:I.414, A:G.442, A:G.442, A:G.444, A:S.445, A:N.470, A:N.470, A:T.474, A:I.475 Water bridges: A:S.390, A:D.443, A:S.445, A:S.445 TPP.4: 21 residues within 4Å: Chain A: P.25, G.26, E.50, V.75, H.114 Chain B: G.388, T.389, G.412, S.413, I.414, G.442, D.443, G.444, S.445, N.470, G.472, Y.473, T.474, I.475, E.476 Ligands: MG.3 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.414, B:Y.473, B:Y.473, A:V.75 Hydrogen bonds: B:T.389, B:G.412, B:I.414, B:G.442, B:G.444, B:S.445, B:N.470, B:T.474, B:I.475 Water bridges: B:T.389, B:S.390, B:G.442, B:D.443, B:D.443, B:S.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arjunan, P. et al., Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 A resolution. J.Mol.Biol. (1996)

Release Date

1995-07-31

Peptides

PYRUVATE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRUVATE DECARBOXYLASE