SMTL ID : 1w88.1 (1 other biounit)

The crystal structure of pyruvate dehydrogenase E1(D180N,E183Q) bound to the peripheral subunit binding domain of E2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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.173, N.202, F.204 Ligands: TPP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.173, A:F.204 MG.3: 4 residues within 4Å: Chain C: D.173, N.202, F.204 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.173, C:F.204, H2O.13

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 20 residues within 4Å: Chain A: Y.102, R.103, I.142, I.144, G.172, D.173, G.174, G.175, Q.178, N.202, F.204, A.205, I.206 Chain D: E.28, L.57, E.59, Q.81, F.85, E.88 Ligands: MG.1 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.144, A:I.206, A:I.206, D:L.57 Hydrogen bonds: A:Y.102, A:Y.102, A:I.142, A:I.144, A:G.172, A:G.174, A:G.175 Water bridges: A:R.103 Salt bridges: A:R.103 pi-Stacking: D:F.85 TPP.4: 20 residues within 4Å: Chain B: E.28, L.57, E.59, Q.81, F.85 Chain C: Y.102, R.103, I.142, I.144, G.172, D.173, G.174, G.175, Q.178, N.202, F.204, A.205, I.206, R.267 Ligands: MG.3 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.144, C:A.205, C:I.206, C:I.206 Hydrogen bonds: C:Y.102, C:Y.102, C:I.142, C:I.144, C:G.172, C:D.173, C:G.174, C:G.175, C:N.202 Water bridges: C:D.173, C:I.206, C:R.267, C:R.267 Salt bridges: C:R.103, C:R.267 pi-Stacking: B:F.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frank, R.A.W. et al., A Molecular Switch and Proton-Wire Synchronize the Active Sites in Thiamine-Dependent Enzymes. Science (2004)

Release Date

2004-11-02

Peptides

PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT: AC
PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT: BD
DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
I

PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT

PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT

DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE

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