SMTL ID : 8p5v.1

Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum in complex with the product succinyl-CoA

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 2.07 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: TPP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.647, A:I.682 MG.5: 4 residues within 4Å: Chain B: D.647, N.680, I.682 Ligands: TPP.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.647, B:I.682 MG.9: 4 residues within 4Å: Chain C: D.647, N.680, I.682 Ligands: TPP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.647, C:I.682 MG.13: 4 residues within 4Å: Chain D: D.647, N.680, I.682 Ligands: TPP.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.647, D:I.682 MG.17: 4 residues within 4Å: Chain E: D.647, N.680, I.682 Ligands: TPP.19 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.647, E:I.682 MG.21: 4 residues within 4Å: Chain F: D.647, N.680, I.682 Ligands: TPP.23 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 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.829, A:P.1141 Hydrogen bonds: A:G.832, A:T.1037, A:R.1053, A:S.1092, A:I.1142, A:N.1145, A:N.1145, A:R.1146 Water bridges: A:H.831, A:G.1034, A:R.1053, A:R.1053, A:S.1092 Salt bridges: A:H.831, A:K.1089, A:R.1146, A:R.1146 pi-Cation interactions: A:R.1053 ACO.6: 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 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.824 Hydrogen bonds: B:G.832, B:T.1037, B:T.1037, B:R.1053, B:S.1092, B:N.1145, B:N.1145, B:R.1146 Water bridges: B:G.1034, B:R.1053, B:R.1053, B:S.1092, B:S.1092 Salt bridges: B:H.831, B:K.1089, B:R.1146, B:R.1146 pi-Cation interactions: B:R.1053 ACO.10: 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 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.832, C:T.1037, C:R.1053, C:S.1092, C:I.1142, C:N.1145, C:R.1146 Water bridges: C:R.1053, C:R.1053 Salt bridges: C:H.831, C:K.1089, C:R.1146, C:R.1146 pi-Cation interactions: C:R.1053 ACO.14: 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 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:T.824, D:P.1141 Hydrogen bonds: 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 Water bridges: D:L.833, D:G.1034, D:S.1092 Salt bridges: D:H.831, D:K.1089, D:R.1146, D:R.1146 pi-Cation interactions: D:R.1053 ACO.18: 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 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:L.829, E:L.1059 Hydrogen bonds: E:G.832, E:T.1037, E:R.1053, E:S.1092, E:I.1142, E:N.1145, E:N.1145, E:R.1146 Water bridges: E:R.1053, E:R.1053, E:S.1092 Salt bridges: E:H.831, E:K.1089, E:R.1146, E:R.1146 pi-Cation interactions: E:R.1053 ACO.22: 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 21 PLIP interactions: 21 interactions with chain F Hydrophobic interactions: F:P.1141 Hydrogen bonds: 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 Water bridges: F:L.833, F:R.1053, F:R.1053, F:K.1089, F:S.1092, 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 TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 20 residues within 4Å: Chain A: H.545, R.546, 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.979 Ligands: MG.1 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:H.749 Water bridges: A:G.646 Salt bridges: A:H.545, A:R.546 Hydrophobic interactions: B:L.949 pi-Stacking: B:F.979 TPP.7: 20 residues within 4Å: Chain A: E.903, L.949, E.951, Q.975, F.979 Chain B: H.545, R.546, 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.5 12 PLIP interactions: 10 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, B:N.680 Water bridges: B:G.646 Salt bridges: B:H.545, B:R.546 Hydrophobic interactions: A:L.949 pi-Stacking: A:F.979 TPP.11: 20 residues within 4Å: Chain C: H.545, R.546, 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.979 Ligands: MG.9 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.610, C:L.612, C:D.647, C:A.648, C:A.649, C:H.749 Water bridges: C:G.646 Salt bridges: C:H.545, C:R.546 Hydrophobic interactions: D:L.949 pi-Stacking: D:F.979 TPP.15: 20 residues within 4Å: Chain C: E.903, L.949, E.951, Q.975, F.979 Chain D: H.545, R.546, 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.13 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.610, D:L.612, D:D.647, D:A.648, D:A.649, D:N.680, D:N.680 Water bridges: D:G.646 Salt bridges: D:H.545, D:R.546 Hydrophobic interactions: C:L.949 pi-Stacking: C:F.979 TPP.19: 20 residues within 4Å: Chain E: H.545, R.546, 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.979 Ligands: MG.17 10 PLIP interactions: 8 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:H.749 Salt bridges: E:H.545, E:R.546 Hydrophobic interactions: F:L.949 pi-Stacking: F:F.979 TPP.23: 20 residues within 4Å: Chain E: E.903, L.949, E.951, Q.975, F.979 Chain F: H.545, R.546, 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.21 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.610, F:L.612, F:D.647, F:A.648, F:A.649, F:N.680, F:N.680 Water bridges: F:G.646 Salt bridges: F:H.545, F:R.546 pi-Stacking: E:F.979

6 x SCA: SUCCINYL-COENZYME A(Non-covalent)

SCA.4: 26 residues within 4Å: Chain A: R.144, K.158, S.160, F.161, T.162, A.203, I.204, D.205, L.215, Y.235, V.239, T.260, N.261, P.262, G.263, G.264, S.270, P.272, V.284, G.285, S.286, M.287 Chain E: T.130, S.131, Y.316, G.323 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:I.204, A:V.239, A:P.272 Hydrogen bonds: A:S.160, A:S.160, A:T.162, A:A.203, A:D.205, A:R.243, A:T.260, A:T.260, A:N.261, A:S.270, A:S.270, A:G.285, A:M.287 Salt bridges: A:R.144, A:K.158 Water bridges: E:S.131, E:S.131, E:A.324 SCA.8: 26 residues within 4Å: Chain B: R.144, K.158, S.160, F.161, T.162, A.203, I.204, D.205, L.215, Y.235, V.239, T.260, N.261, P.262, G.263, G.264, S.270, P.272, V.284, G.285, S.286, M.287 Chain D: T.130, S.131, Y.316, G.323 22 PLIP interactions: 18 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:I.204, B:V.239, B:P.272 Hydrogen bonds: B:S.160, B:S.160, B:T.162, B:A.203, B:D.205, B:Y.235, B:T.260, B:T.260, B:N.261, B:S.270, B:S.270, B:G.285, B:M.287, D:Y.316 Salt bridges: B:R.144, B:K.158 Water bridges: D:S.131, D:S.131, D:A.324 SCA.12: 26 residues within 4Å: Chain A: T.130, S.131, Y.316, G.323 Chain C: R.144, K.158, S.160, F.161, T.162, A.203, I.204, D.205, L.215, Y.235, V.239, T.260, N.261, P.262, G.263, G.264, S.270, P.272, V.284, G.285, S.286, M.287 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:I.204, C:V.239, C:P.272 Hydrogen bonds: C:S.160, C:S.160, C:T.162, C:A.203, C:D.205, C:T.260, C:T.260, C:N.261, C:S.270, C:S.270, C:G.285, C:M.287 Salt bridges: C:R.144, C:K.158 Water bridges: A:S.131, A:S.131 SCA.16: 26 residues within 4Å: Chain D: R.144, K.158, S.160, F.161, T.162, A.203, I.204, D.205, L.215, Y.235, V.239, T.260, N.261, P.262, G.263, G.264, S.270, P.272, V.284, G.285, S.286, M.287 Chain F: T.130, S.131, Y.316, G.323 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:I.204, D:V.239, D:P.272 Hydrogen bonds: D:S.160, D:S.160, D:A.203, D:D.205, D:Y.235, D:T.260, D:T.260, D:N.261, D:S.270, D:S.270, D:G.285, D:M.287, F:Y.316 Salt bridges: D:R.144, D:K.158 Water bridges: F:S.131, F:S.131 SCA.20: 27 residues within 4Å: Chain C: T.130, S.131, Y.316, G.323 Chain E: R.144, K.158, S.160, F.161, T.162, A.203, I.204, D.205, L.215, Y.235, V.239, R.243, T.260, N.261, P.262, G.263, G.264, S.270, P.272, V.284, G.285, S.286, M.287 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:I.204, E:V.239, E:P.272 Hydrogen bonds: E:S.160, E:S.160, E:T.162, E:A.203, E:D.205, E:R.243, E:T.260, E:T.260, E:N.261, E:S.270, E:S.270, E:G.285, E:M.287 Salt bridges: E:R.144, E:K.158 Water bridges: C:S.131, C:S.131 SCA.24: 27 residues within 4Å: Chain B: T.130, S.131, Y.316, G.323 Chain F: R.144, K.158, S.160, F.161, T.162, A.203, I.204, D.205, L.215, Y.235, V.239, R.243, T.260, N.261, P.262, G.263, G.264, S.270, P.272, V.284, G.285, S.286, M.287 22 PLIP interactions: 19 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:Y.235, F:V.239, F:P.272 Hydrogen bonds: F:S.160, F:S.160, F:T.162, F:A.203, F:D.205, F:Y.235, F:R.243, F:T.260, F:T.260, F:N.261, F:S.270, F:S.270, F:G.285, F:M.287, B:Y.316 Salt bridges: F:R.144, F:K.158 Water bridges: B:S.131, B:S.131

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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