SMTL ID : 3duf.2 (1 other biounit)

Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.174, N.203, F.205 Ligands: R1T.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.174, A:F.205, H2O.1 MG.3: 4 residues within 4Å: Chain C: D.174, N.203, F.205 Ligands: R1T.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.174, C:F.205, H2O.5

2 x R1T: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

R1T.2: 20 residues within 4Å: Chain A: Y.103, R.104, I.143, I.145, G.173, D.174, G.175, G.176, N.203, F.205, A.206, I.207, H.272 Chain D: E.29, L.58, E.60, Q.82, F.86, H.129 Ligands: MG.1 20 PLIP interactions: 3 interactions with chain D, 17 interactions with chain A Hydrophobic interactions: D:L.58, D:F.86, A:Y.103, A:I.143, A:I.207, A:I.207 pi-Stacking: D:F.86 Hydrogen bonds: A:Y.103, A:Y.103, A:I.143, A:I.145, A:G.173, A:D.174, A:G.175, A:G.176, A:F.205 Water bridges: A:I.207, A:R.268 Salt bridges: A:R.104, A:H.272 R1T.4: 20 residues within 4Å: Chain B: E.29, L.58, E.60, Q.82, F.86, H.129 Chain C: Y.103, R.104, I.143, I.145, G.173, D.174, G.175, G.176, N.203, F.205, A.206, I.207, H.272 Ligands: MG.3 20 PLIP interactions: 2 interactions with chain B, 18 interactions with chain C Hydrophobic interactions: B:L.58, C:Y.103, C:I.143, C:I.145, C:I.207, C:I.207 pi-Stacking: B:F.86 Hydrogen bonds: C:Y.103, C:Y.103, C:I.143, C:I.145, C:G.173, C:G.173, C:D.174, C:G.175, C:G.176, C:N.203 Water bridges: C:R.104, C:I.207 Salt bridges: C:R.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pei, X.Y. et al., Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex. Structure (2008)

Release Date

2009-01-06

Peptides

Pyruvate dehydrogenase E1 component subunit alpha: AC
Pyruvate dehydrogenase E1 component subunit beta: BD
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

C
G

B
F

D
H

E
J

Pyruvate dehydrogenase E1 component subunit alpha

Pyruvate dehydrogenase E1 component subunit beta

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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