SMTL ID : 2w93.1 (1 other biounit)

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 20 residues within 4Å: Chain A: 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, Q.477 Chain B: P.26, G.27, E.51, V.76 Ligands: MG.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.415, A:I.415, A:Y.474, A:Y.474, A:I.476, B:V.76 Hydrogen bonds: A:T.390, A:G.413, A:I.415, A:G.443, A:G.445, A:S.446, A:N.471, A:T.475, A:I.476 Water bridges: A:T.390, A:S.391, A:D.444, A:S.446, A:S.446 TPP.5: 23 residues within 4Å: Chain A: P.26, G.27, E.51, V.76, H.115 Chain B: 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, Q.477 Ligands: MG.6, PY0.7 20 PLIP interactions: 1 interactions with chain A, 19 interactions with chain B Hydrophobic interactions: A:V.76, B:I.415, B:I.415, B:L.449, 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:T.475, B:I.476 Water bridges: B:T.390, B:S.391, B:G.443, B:D.444, B:S.446

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.444, N.471, G.473 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:G.473, H2O.14 MG.6: 4 residues within 4Å: Chain B: D.444, N.471, G.473 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.444, B:G.473, H2O.26

4 x PY0: (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate

PY0.3: 8 residues within 4Å: Chain A: H.92, C.221, H.225, G.286, A.287, H.310, S.311, D.312 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:H.92, A:A.287, A:H.310, A:S.311, A:D.312 Water bridges: A:S.311 Salt bridges: A:H.225, A:H.310 PY0.4: 3 residues within 4Å: Chain A: Q.16, V.17, M.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.16, A:V.17 Water bridges: A:V.17, A:K.65 PY0.7: 9 residues within 4Å: Chain A: G.27, D.28, H.115 Chain B: F.292, T.388, I.476, Q.477, I.480 Ligands: TPP.5 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.28, A:D.28, A:D.28, B:Q.477, B:Q.477 Hydrophobic interactions: B:T.388, B:I.476 PY0.8: 8 residues within 4Å: Chain B: H.92, C.221, H.225, G.286, A.287, H.310, S.311, D.312 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.310, B:S.311 Salt bridges: B:H.92, B:H.225, B:H.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Konig, S. et al., Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story. J.Mol.Catal., B Enzym. (2014)

Release Date

2009-02-03

Peptides

PYRUVATE DECARBOXYLASE ISOZYME 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PYRUVATE DECARBOXYLASE ISOZYME 1

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