SMTL ID : 8p5x.1

Single particle cryo-EM structure of the complex between Corynebacterium glutamicum homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-protein inhibitor OdhI

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.29 Å

Oligo State

hetero-6-6-mer

Ligands

6 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 18 residues within 4Å: Chain A: R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Chain B: E.903, L.949, E.951, Q.975, F.979 Ligands: MG.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.610, A:L.612, A:D.647, A:A.648, A:A.649, A:N.680, A:N.680 Salt bridges: A:R.546, A:H.749 Hydrophobic interactions: B:L.949 pi-Stacking: B:F.979 TPP.3: 18 residues within 4Å: Chain A: E.903, L.949, E.951, Q.975, F.979 Chain B: R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Ligands: MG.4 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.610, B:L.612, B:D.647, B:A.648, B:A.649, B:N.680 Salt bridges: B:R.546 Hydrophobic interactions: A:L.949 pi-Stacking: A:F.979 TPP.6: 18 residues within 4Å: Chain C: R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Chain D: E.903, L.949, E.951, Q.975, F.979 Ligands: MG.5 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: D:L.949 pi-Stacking: D:F.979 Hydrogen bonds: C:S.610, C:L.612, C:D.647, C:A.648, C:A.649, C:N.680, C:N.680 Salt bridges: C:R.546, C:H.749 TPP.7: 18 residues within 4Å: Chain C: E.903, L.949, E.951, Q.975, F.979 Chain D: R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Ligands: MG.8 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.949 pi-Stacking: C:F.979 Hydrogen bonds: D:S.610, D:L.612, D:D.647, D:A.648, D:A.649, D:N.680 Salt bridges: D:R.546 TPP.9: 18 residues within 4Å: Chain E: R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Chain F: E.903, L.949, E.951, Q.975, F.979 Ligands: MG.10 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:S.610, E:L.612, E:D.647, E:A.648, E:A.649, E:N.680, E:N.680 Salt bridges: E:R.546, E:H.749 Hydrophobic interactions: F:L.949 pi-Stacking: F:F.979 TPP.11: 18 residues within 4Å: Chain E: E.903, L.949, E.951, Q.975, F.979 Chain F: R.546, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, H.749 Ligands: MG.12 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.610, F:L.612, F:D.647, F:A.648, F:A.649, F:N.680 Salt bridges: F:R.546, F:H.749 Hydrophobic interactions: E:L.949 pi-Stacking: E:F.979

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.647, N.680, I.682 Ligands: TPP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.682 MG.4: 4 residues within 4Å: Chain B: D.647, N.680, I.682 Ligands: TPP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:I.682 MG.5: 4 residues within 4Å: Chain C: D.647, N.680, I.682 Ligands: TPP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:I.682 MG.8: 4 residues within 4Å: Chain D: D.647, N.680, I.682 Ligands: TPP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:I.682 MG.10: 4 residues within 4Å: Chain E: D.647, N.680, I.682 Ligands: TPP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:I.682 MG.12: 4 residues within 4Å: Chain F: D.647, N.680, I.682 Ligands: TPP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:I.682

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, L. et al., High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase. Nat Commun (2023)

Release Date

2023-08-16

Peptides

2-oxoglutarate dehydrogenase E1/E2 component: ABCDEF
Oxoglutarate dehydrogenase inhibitor: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

2-oxoglutarate dehydrogenase E1/E2 component

Oxoglutarate dehydrogenase inhibitor

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