SMTL ID : 1w85.2 (1 other biounit)

The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: D.173, N.202 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:D.173, H2O.4 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain C: D.173, N.202, F.204, A.205 Ligands: TPP.7 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.173, C:D.173, C:F.204, H2O.17

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 18 residues within 4Å: Chain A: Y.102, R.103, I.142, I.143, I.144, G.172, D.173, G.174, G.175, Q.178, N.202, H.271 Chain D: E.28, L.57, E.59, Q.81, F.85 Ligands: MG.1 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.143, A:I.144, D:L.57 Hydrogen bonds: A:Y.102, A:I.142, A:I.144, A:G.172, A:G.174, A:G.175, A:Q.178, A:H.271 Water bridges: A:Q.81, A:R.103, A:D.173, A:D.173 Salt bridges: A:R.103 pi-Stacking: D:F.85 TPP.7: 21 residues within 4Å: Chain B: E.28, L.57, E.59, Q.81, F.85 Chain C: Y.102, R.103, I.142, I.143, I.144, G.172, D.173, G.174, G.175, Q.178, N.202, F.204, A.205, I.206, H.271 Ligands: MG.5 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.143, C:I.144, C:I.206, C:I.206 Hydrogen bonds: C:Y.102, C:I.142, C:I.144, C:G.172, C:G.174, C:G.175, C:Q.178, C:N.202 Water bridges: C:Q.81, C:R.103, C:R.103, C:D.173, C:N.202, C:F.204 Salt bridges: C:R.103, C:H.271 pi-Stacking: B:F.85

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain B: P.111, I.112, T.113, A.160, D.163, D.165, V.167 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.160, B:D.163, B:D.165, H2O.8 K.8: 7 residues within 4Å: Chain D: P.111, I.112, T.113, A.160, D.163, D.165, V.167 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:I.112, D:A.160, D:D.163, D:D.165, H2O.24

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain C: I.109, W.110, G.112, L.113, P.114, E.324 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.324 Water bridges: C:L.115, C:Q.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frank, R.A. et al., A molecular switch and proton wire synchronize the active sites in thiamine 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
E

C
G

B
F

D
H

E
J

PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT

PYRUVATE DEHYDROGENASE E1 COMPONENT, BETA SUBUNIT

DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE

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