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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-2-2-1-mer

Ligands

2 x TPW: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TPW.1: 22 residues within 4Å: Chain A: Y.103, R.104, I.143, I.144, I.145, G.173, D.174, G.175, G.176, Q.179, N.203, F.205, A.206, A.207, R.268, H.272 Chain D: E.29, L.58, E.60, Q.82, F.86 Ligands: MG.2 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.144, A:I.145, D:F.86 Hydrogen bonds: A:Y.103, A:I.143, A:I.145, A:G.173, A:G.175, A:G.176, A:N.203, A:F.205, A:A.207 Water bridges: A:R.268 Salt bridges: A:R.104, A:R.268, A:H.272 pi-Stacking: D:F.86 TPW.4: 22 residues within 4Å: Chain B: E.29, L.58, E.60, Q.82, F.86, E.89 Chain C: Y.103, R.104, I.143, I.144, I.145, G.173, D.174, G.175, G.176, Q.179, N.203, F.205, A.206, A.207, H.272 Ligands: MG.5 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.144, C:I.145, C:A.207, B:L.58, B:F.86 Hydrogen bonds: C:Y.103, C:I.143, C:I.145, C:G.173, C:G.175, C:G.176, C:N.203, C:F.205, C:F.205, C:A.207 Water bridges: C:R.104, C:R.104, C:N.203 Salt bridges: C:R.104, C:H.272 pi-Stacking: B:F.86

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 6 residues within 4Å: Chain A: G.173, D.174, Q.201, N.203, F.205 Ligands: TPW.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.174 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain C: D.174, N.203, F.205, A.206 Ligands: TPW.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.174, C:F.205, H2O.11

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

2009-01-13

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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