SMTL ID : 7wgr.1

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: H.15, D.28, D.30, S.32 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.15, A:D.30 CA.4: 4 residues within 4Å: Chain B: H.15, D.28, D.30, S.32 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.15, B:D.28, B:D.30

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.283, N.316, I.318 Ligands: TPP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.318 MG.5: 4 residues within 4Å: Chain B: D.283, N.316, I.318 Ligands: TPP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.318

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 18 residues within 4Å: Chain A: R.184, S.247, L.249, G.282, D.283, A.284, A.285, Q.289, N.316, I.318, G.319, H.385 Chain B: Q.548, L.592, E.594, Q.618, F.622 Ligands: MG.2 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:L.249, A:A.284, A:A.285, A:N.316, A:F.320, A:H.385, B:Q.548, B:Q.618 Salt bridges: A:R.184 Hydrophobic interactions: B:L.592, B:F.622 pi-Stacking: B:F.622 TPP.6: 17 residues within 4Å: Chain A: Q.548, L.592, E.594, Q.618, F.622 Chain B: R.184, L.249, G.282, D.283, A.284, A.285, Q.289, N.316, I.318, G.319, H.385 Ligands: MG.5 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:L.249, B:A.284, B:A.285, B:N.316, A:Q.618 Salt bridges: B:R.184 Hydrophobic interactions: A:L.592, A:F.622 pi-Stacking: A:F.622

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, Y. et al., Structural basis for the activity and regulation of human alpha-ketoglutarate dehydrogenase revealed by Cryo-EM. Biochem.Biophys.Res.Commun. (2022)

Release Date

2022-06-01

Peptides

2-oxoglutarate dehydrogenase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-oxoglutarate dehydrogenase, mitochondrial