SMTL ID : 1ni4.1

HUMAN PYRUVATE DEHYDROGENASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: D.171, N.200, Y.202 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.171, C:Y.202, H2O.15 MG.4: 4 residues within 4Å: Chain A: D.171, N.200, Y.202 Ligands: TPP.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.171, A:D.171, A:Y.202, H2O.1

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 20 residues within 4Å: Chain A: Y.93, R.94, G.140, I.141, V.142, G.170, D.171, G.172, A.173, N.200, Y.202, G.203, H.267 Chain D: E.40, I.69, E.71, M.93, F.97, Q.100 Ligands: MG.4 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.141 Hydrogen bonds: A:Y.93, A:G.140, A:V.142, A:G.170, A:D.171, A:G.172, A:A.173, A:N.200, A:N.200 Water bridges: A:Q.72, A:R.94, A:D.171, A:N.200, A:H.267 Salt bridges: A:R.94, A:H.267 pi-Stacking: D:F.97 TPP.5: 21 residues within 4Å: Chain B: E.40, I.69, E.71, M.93, F.97, Q.100 Chain C: Y.93, R.94, G.140, I.141, V.142, G.170, D.171, G.172, A.173, N.200, Y.202, G.203, M.204, H.267 Ligands: MG.1 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.141 Hydrogen bonds: C:Y.93, C:G.140, C:V.142, C:G.170, C:D.171, C:G.172, C:A.173, C:N.200, C:N.200 Water bridges: C:D.171, C:D.171, C:H.267, C:H.267 Salt bridges: C:R.94, C:H.267 pi-Stacking: B:F.97

2 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain B: P.123, I.124, V.125, A.172, D.175, N.177, V.179 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.172, B:N.177, H2O.8 K.6: 7 residues within 4Å: Chain D: P.123, I.124, V.125, A.172, D.175, N.177, V.179 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:A.172, D:D.175, D:N.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ciszak, E.M. et al., Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase. J.Biol.Chem. (2003)

Release Date

2003-06-17

Peptides

Pyruvate dehydrogenase E1 component: Alpha subunit: AC
Pyruvate dehydrogenase E1 component: Beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Pyruvate dehydrogenase E1 component: Alpha subunit

Pyruvate dehydrogenase E1 component: Beta subunit

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