SMTL ID : 8p5w.1

Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.26 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.647, N.680, I.682 Ligands: QSP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.647, A:I.682 MG.4: 4 residues within 4Å: Chain B: D.647, N.680, I.682 Ligands: QSP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.647, B:I.682 MG.7: 4 residues within 4Å: Chain C: D.647, N.680, I.682 Ligands: QSP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.647, C:I.682 MG.10: 4 residues within 4Å: Chain D: D.647, N.680, I.682 Ligands: QSP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.647, D:I.682 MG.13: 4 residues within 4Å: Chain E: D.647, N.680, I.682 Ligands: QSP.15 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.647, E:I.682 MG.16: 4 residues within 4Å: Chain F: D.647, N.680, I.682 Ligands: QSP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.647, F:I.682

6 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.2: 20 residues within 4Å: Chain A: T.824, L.829, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.832, A:T.1037, A:T.1037, A:R.1053, A:R.1061, A:S.1092, A:I.1142, A:N.1145, A:N.1145, A:R.1146 Salt bridges: A:H.831, A:K.1089, A:R.1146, A:R.1146 pi-Cation interactions: A:R.1053 ACO.5: 20 residues within 4Å: Chain B: T.824, L.829, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.824, B:G.832, B:T.1037, B:T.1037, B:R.1053, B:S.1092, B:I.1142, B:N.1145, B:N.1145, B:R.1146 Salt bridges: B:H.831, B:K.1089, B:R.1146, B:R.1146 pi-Cation interactions: B:R.1053 ACO.8: 20 residues within 4Å: Chain C: T.824, L.829, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:G.832, C:T.1037, C:T.1037, C:R.1053, C:R.1061, C:S.1092, C:I.1142, C:N.1145, C:N.1145, C:R.1146 Salt bridges: C:H.831, C:K.1089, C:R.1146, C:R.1146 pi-Cation interactions: C:R.1053 ACO.11: 20 residues within 4Å: Chain D: T.824, L.829, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.824, D:G.832, D:T.1037, D:T.1037, D:R.1053, D:S.1092, D:I.1142, D:N.1145, D:N.1145, D:R.1146 Salt bridges: D:H.831, D:K.1089, D:R.1146, D:R.1146 pi-Cation interactions: D:R.1053 ACO.14: 20 residues within 4Å: Chain E: T.824, L.829, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.832, E:T.1037, E:T.1037, E:R.1053, E:R.1061, E:S.1092, E:I.1142, E:N.1145, E:N.1145, E:R.1146 Salt bridges: E:H.831, E:K.1089, E:R.1146, E:R.1146 pi-Cation interactions: E:R.1053 ACO.17: 20 residues within 4Å: Chain F: T.824, L.829, P.830, H.831, G.832, G.1034, M.1036, T.1037, R.1053, L.1059, R.1061, K.1089, S.1092, M.1138, P.1141, I.1142, P.1143, F.1144, N.1145, R.1146 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:T.824, F:G.832, F:T.1037, F:T.1037, F:R.1053, F:S.1092, F:I.1142, F:N.1145, F:N.1145, F:R.1146 Salt bridges: F:H.831, F:K.1089, F:R.1146, F:R.1146 pi-Cation interactions: F:R.1053

6 x QSP: (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid(Non-covalent)

QSP.3: 23 residues within 4Å: Chain A: H.545, R.546, H.585, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, F.684, H.749 Chain B: E.903, L.949, E.951, Q.975, F.976, F.979, H.1019 Ligands: MG.1 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:L.949 pi-Stacking: B:F.979 Hydrogen bonds: A:S.610, A:L.612, A:D.647, A:A.648, A:A.649, A:H.749, A:H.749 Salt bridges: A:H.545, A:H.545, A:R.546, A:H.585 QSP.6: 23 residues within 4Å: Chain A: E.903, L.949, E.951, Q.975, F.976, F.979, H.1019 Chain B: H.545, R.546, H.585, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, F.684, H.749 Ligands: MG.4 13 PLIP interactions: 2 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:L.949 pi-Stacking: A:F.979 Hydrogen bonds: B:S.610, B:L.612, B:D.647, B:A.648, B:A.649, B:N.680, B:H.749 Salt bridges: B:H.545, B:H.545, B:R.546, B:H.585 QSP.9: 24 residues within 4Å: Chain C: F.512, H.545, R.546, H.585, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, F.684, H.749 Chain D: E.903, L.949, E.951, Q.975, F.976, F.979, H.1019 Ligands: MG.7 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.512, D:L.949 Hydrogen bonds: C:S.610, C:L.612, C:D.647, C:A.648, C:A.649, C:H.749, C:H.749 Salt bridges: C:H.545, C:H.545, C:R.546, C:H.585 pi-Stacking: D:F.979 QSP.12: 24 residues within 4Å: Chain C: E.903, L.949, E.951, Q.975, F.976, F.979, H.1019 Chain D: F.512, H.545, R.546, H.585, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, F.684, H.749 Ligands: MG.10 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.512, C:L.949 Hydrogen bonds: D:S.610, D:L.612, D:D.647, D:A.648, D:A.649, D:N.680, D:H.749 Salt bridges: D:H.545, D:H.545, D:R.546, D:H.585 pi-Stacking: C:F.979 QSP.15: 23 residues within 4Å: Chain E: H.545, R.546, H.585, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, F.684, H.749 Chain F: E.903, L.949, E.951, Q.975, F.976, F.979, H.1019 Ligands: MG.13 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:K.510, E:S.610, E:L.612, E:D.647, E:D.647, E:A.648, E:A.649, E:H.749, E:H.749 Salt bridges: E:H.545, E:H.545, E:R.546, E:H.585 Hydrophobic interactions: F:L.949 pi-Stacking: F:F.979 QSP.18: 23 residues within 4Å: Chain E: E.903, L.949, E.951, Q.975, F.976, F.979, H.1019 Chain F: H.545, R.546, H.585, S.610, H.611, L.612, G.646, D.647, A.648, A.649, N.680, I.682, G.683, F.684, H.749 Ligands: MG.16 13 PLIP interactions: 2 interactions with chain E, 11 interactions with chain F Hydrophobic interactions: E:L.949 pi-Stacking: E:F.979 Hydrogen bonds: F:S.610, F:L.612, F:D.647, F:A.648, F:A.649, F:N.680, F:H.749 Salt bridges: F:H.545, F:H.545, F:R.546, F:H.585

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

2-oxoglutarate dehydrogenase E1/E2 component

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