SMTL ID : 1qpb.2 (1 other biounit)

PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 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, T.73, V.76, H.115 Ligands: MG.2, PYM.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.415, A:I.415, A:L.449, A:Y.474, A:Y.474 Hydrogen bonds: A:T.390, A:G.413, A:I.415, A:G.443, A:G.445, A:S.446, A:N.471, A:N.471, A:T.475, A:I.476 Water bridges: A:G.443, A:D.444, A:D.444 TPP.4: 21 residues within 4Å: Chain A: P.26, G.27, E.51, T.73, V.76, G.77 Chain B: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, N.471, G.473, Y.474, T.475, I.476 Ligands: MG.5 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.474, B:Y.474, A:V.76 Hydrogen bonds: B:T.390, B:T.390, B:G.413, B:I.415, B:G.445, B:S.446, B:N.471, B:N.471, B:T.475, B:I.476 Water bridges: B:G.443, B:D.444, B:D.444

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.444, N.471, G.473, T.475 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:G.473, H2O.3 MG.5: 6 residues within 4Å: Chain B: D.444, N.471, G.473, Y.474, T.475 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.444, B:G.473, H2O.5

2 x PYM: PYRUVAMIDE(Non-covalent)

PYM.3: 6 residues within 4Å: Chain A: Y.157, V.158, Q.160, R.224, H.225, D.226 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.226 Hydrogen bonds: A:Q.160, A:R.224 PYM.6: 6 residues within 4Å: Chain A: E.477 Chain B: G.27, D.28, H.114, H.115 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.28 Water bridges: B:D.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, G. et al., The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase a Crystallographic and Kinetic Study. Eur.J.Biochem. (2000)

Release Date

2000-02-04

Peptides

PYRUVATE DECARBOXYLASE (FORM B): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRUVATE DECARBOXYLASE (FORM B)

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