SMTL ID : 1pyd.1

CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.444, L.469, N.471, G.473 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:G.473, H2O.1 MG.3: 4 residues within 4Å: Chain B: D.444, N.471, G.473 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.444, B:G.473, H2O.1

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 21 residues within 4Å: Chain A: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Chain B: P.26, G.27, E.51, V.76 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.415, A:L.449, A:Y.474, A:Y.474 Hydrogen bonds: A:T.390, A:T.390, A:G.413, A:I.415, A:G.443, A:G.445, A:S.446, A:N.471, A:G.473, A:T.475, A:I.476 Water bridges: A:D.444 TPP.4: 22 residues within 4Å: Chain A: P.26, G.27, E.51, V.76 Chain B: T.388, G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.415, B:L.449, B:Y.474, B:Y.474, B:I.476 Hydrogen bonds: B:T.390, B:G.413, B:I.415, B:G.443, B:G.445, B:S.446, B:N.471, B:G.473, B:T.475, B:I.476 Water bridges: B:D.444, B:D.444

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dyda, F. et al., Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution. Biochemistry (1993)

Release Date

1994-04-30

Peptides

PYRUVATE DECARBOXYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRUVATE DECARBOXYLASE