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

Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.188, N.217, Y.219 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.188, A:Y.219, H2O.1 MN.5: 5 residues within 4Å: Chain C: D.188, N.217, Y.219, G.220 Ligands: TPP.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.188, C:Y.219, H2O.24

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 22 residues within 4Å: Chain A: Y.110, R.111, G.157, I.158, V.159, G.187, D.188, G.189, A.190, N.217, Y.219, G.220, M.221, H.284 Chain D: E.28, I.57, E.59, M.81, F.85, Q.88, H.128 Ligands: MN.1 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.158, A:M.221 Hydrogen bonds: A:Y.110, A:G.157, A:V.159, A:G.187, A:G.189, A:A.190, A:N.217, A:M.221 Water bridges: A:R.111, A:D.188, A:D.188, A:R.280 Salt bridges: A:R.111, A:H.284 pi-Stacking: D:F.85 TPP.6: 23 residues within 4Å: Chain B: E.28, I.57, E.59, M.81, F.85, Q.88, H.128 Chain C: Y.110, R.111, G.157, I.158, V.159, G.187, D.188, G.189, A.190, Q.193, N.217, Y.219, G.220, M.221, H.284 Ligands: MN.5 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.158, C:M.221 Hydrogen bonds: C:Y.110, C:G.157, C:V.159, C:G.187, C:G.189, C:A.190, C:M.221 Water bridges: C:Q.89, C:R.111, C:D.188, C:D.188, C:H.284 Salt bridges: C:R.111, C:H.284 pi-Stacking: B:F.85

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: K.174, W.206, L.208 Chain B: D.49, K.50, I.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.174, A:K.174 GOL.7: 6 residues within 4Å: Chain C: L.171, K.174, W.206, L.208 Chain D: D.49, I.53 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.174 Water bridges: D:D.49, D:D.49

2 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain B: R.75, V.113, A.160, I.161, D.163 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.160, B:I.161, B:D.163, H2O.14, H2O.15 K.8: 5 residues within 4Å: Chain D: R.75, V.113, A.160, I.161, D.163 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:A.160, D:I.161, D:D.163, H2O.36, H2O.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, M. et al., Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops. Structure (2008)

Release Date

2008-11-25

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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