SMTL ID : 6cfo.1

HUMAN PYRUVATE DEHYDROGENASE E1 COMPONENT COMPLEX WITH COVALENT TDP ADDUCT ACETYL PHOSPHINATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x A5X: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium(Non-covalent)

A5X.1: 24 residues within 4Å: Chain A: F.65, H.67, 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 Chain D: E.40, I.69, E.71, M.93, F.97, Q.100, H.140 Ligands: MG.2 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.93, A:I.141, A:V.142, A:M.204 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:M.204 Water bridges: A:R.94, A:S.268 Salt bridges: A:R.94, A:H.267 pi-Stacking: D:F.97 A5X.3: 24 residues within 4Å: Chain B: E.40, I.69, E.71, M.93, F.97, Q.100, H.140 Chain C: F.65, H.67, Y.93, R.94, G.140, V.142, G.170, D.171, G.172, A.173, Q.176, N.200, Y.202, G.203, M.204, H.267 Ligands: MG.4 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.93, C:V.142 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:M.204 Water bridges: C:R.94 Salt bridges: C:R.94, C:H.267 pi-Stacking: B:F.97

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.171, N.200, Y.202, G.203 Ligands: A5X.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.171, A:Y.202, H2O.2 MG.4: 4 residues within 4Å: Chain C: D.171, N.200, Y.202 Ligands: A5X.3 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.171, C:Y.202, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitley, M.J. et al., Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the alpha V138M variant of human pyruvate dehydrogenase. J. Biol. Chem. (2018)

Release Date

2018-07-11

Peptides

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial: AC
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial

Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

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