SMTL ID : 8i0k.1

Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase(E1) with TCAIM complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.299, N.332, I.334 Ligands: TPP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.299, A:I.334 MG.3: 4 residues within 4Å: Chain B: D.299, N.332, I.334 Ligands: 8EL.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.299, B:I.334

1 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 19 residues within 4Å: Chain A: H.199, R.200, S.263, H.264, L.265, G.298, D.299, A.300, A.301, N.332, I.334, G.335, F.336, H.401 Chain B: L.608, E.610, Q.634, F.638 Ligands: MG.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.263, A:L.265, A:D.299, A:A.300, A:A.301, A:N.332 Salt bridges: A:H.199, A:R.200 Hydrophobic interactions: B:L.608 pi-Stacking: B:F.638

1 x 8EL: 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate(Non-covalent)

8EL.4: 21 residues within 4Å: Chain A: Q.564, L.608, E.610, Q.634, F.638 Chain B: H.199, R.200, S.263, H.264, L.265, G.298, D.299, A.300, A.301, Q.305, N.332, I.334, G.335, F.336, H.401 Ligands: MG.3 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.263, B:L.265, B:G.298, B:D.299, B:A.300, B:A.301, B:N.332, B:N.332 Salt bridges: B:H.199, B:R.200, B:H.401 Hydrophobic interactions: A:L.608 pi-Stacking: A:F.638

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain B: H.31, D.44, D.46 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.31, B:D.44, B:D.44, B:D.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Cryo-electron microscopic structure of the 2-oxoglutarate dehydrogenase (E1) with TCAIM complex. To Be Published

Release Date

2024-05-01

Peptides

2-oxoglutarate dehydrogenase complex component E1: AB
T-cell activation inhibitor, mitochondrial: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2-oxoglutarate dehydrogenase complex component E1

T-cell activation inhibitor, mitochondrial