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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-1-mer

Ligands

3 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.4: 5 residues within 4Å: Chain C: D.174, Q.201, N.203, F.205 Ligands: R1T.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.174, C:F.205 MG.6: 1 residues within 4Å: Chain D: E.89 No protein-ligand interaction detected (PLIP)

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: 23 residues within 4Å: Chain A: Y.103, R.104, I.143, I.145, G.173, D.174, G.175, G.176, Q.179, N.203, F.205, A.206, I.207, R.268, H.272 Chain D: E.29, L.58, E.60, Q.82, F.86, E.89, H.129 Ligands: MG.1 17 PLIP interactions: 3 interactions with chain D, 14 interactions with chain A Hydrophobic interactions: D:L.58, D:F.86, A:I.145, 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:N.203, A:R.268 Water bridges: A:N.203 Salt bridges: A:R.104 R1T.5: 22 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.144, I.145, G.173, D.174, G.175, G.176, Q.179, N.203, F.205, A.206, I.207, H.272 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.103, C:I.207, C:I.207, B:F.86 Hydrogen bonds: C:Y.103, C:Y.103, C:I.143, C:I.145, C:G.173, C:D.174, C:G.175, C:G.176, C:N.203 Salt bridges: C:R.104 pi-Stacking: B:F.86

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain B: P.112, I.113, T.114, A.161, D.164, D.166, V.168 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:A.161, B:D.164, B:D.166 K.7: 7 residues within 4Å: Chain D: P.112, I.113, T.114, A.161, D.164, D.166, V.168 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:I.113, D:A.161, D:D.166

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
A

C
C

B
B

D
D

E
I

Pyruvate dehydrogenase E1 component subunit alpha

Pyruvate dehydrogenase E1 component subunit beta

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

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