SMTL ID : 8p5s.1

Crystal structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-hexamer

Ligands

6 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 6 residues within 4Å: Chain A: P.304, V.305, P.306 Chain E: D.364, K.566, K.637 5 PLIP interactions: 5 interactions with chain E Water bridges: E:D.364, E:K.566 Salt bridges: E:D.364, E:D.364, E:K.637 EPE.6: 6 residues within 4Å: Chain B: P.304, V.305, P.306 Chain D: D.364, K.566, K.637 5 PLIP interactions: 5 interactions with chain D Water bridges: D:D.364, D:K.566 Salt bridges: D:D.364, D:D.364, D:K.637 EPE.11: 6 residues within 4Å: Chain C: P.304, V.305, P.306 Chain F: D.364, K.566, K.637 5 PLIP interactions: 5 interactions with chain F Water bridges: F:D.364, F:K.566 Salt bridges: F:D.364, F:D.364, F:K.637 EPE.16: 6 residues within 4Å: Chain B: D.364, K.566, K.637 Chain D: P.304, V.305, P.306 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.364, B:K.566 Salt bridges: B:D.364, B:D.364, B:K.637 EPE.21: 6 residues within 4Å: Chain A: D.364, K.566, K.637 Chain E: P.304, V.305, P.306 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.364, A:K.566 Salt bridges: A:D.364, A:D.364, A:K.637 EPE.26: 6 residues within 4Å: Chain C: D.364, K.566, K.637 Chain F: P.304, V.305, P.306 5 PLIP interactions: 5 interactions with chain C Water bridges: C:D.364, C:K.566 Salt bridges: C:D.364, C:D.364, C:K.637

6 x COA: COENZYME A(Non-covalent)

COA.2: 12 residues within 4Å: Chain A: R.46, K.60, S.62, F.63, T.64, Y.137, N.163, G.165, G.166, G.187, S.188, M.189 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.46, A:R.46, A:S.62, A:S.62, A:T.64, A:T.64, A:Y.137, A:N.163, A:G.187, A:M.189 Water bridges: A:K.60, A:F.63 Salt bridges: A:R.46, A:K.60 COA.7: 12 residues within 4Å: Chain B: R.46, K.60, S.62, F.63, T.64, Y.137, N.163, G.165, G.166, G.187, S.188, M.189 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.46, B:R.46, B:S.62, B:S.62, B:T.64, B:T.64, B:Y.137, B:N.163, B:G.187, B:M.189 Water bridges: B:K.60, B:F.63 Salt bridges: B:R.46, B:K.60 COA.12: 12 residues within 4Å: Chain C: R.46, K.60, S.62, F.63, T.64, Y.137, N.163, G.165, G.166, G.187, S.188, M.189 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:R.46, C:R.46, C:S.62, C:S.62, C:T.64, C:T.64, C:Y.137, C:N.163, C:G.187, C:M.189 Water bridges: C:K.60, C:F.63 Salt bridges: C:R.46, C:K.60 COA.17: 12 residues within 4Å: Chain D: R.46, K.60, S.62, F.63, T.64, Y.137, N.163, G.165, G.166, G.187, S.188, M.189 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.46, D:R.46, D:S.62, D:S.62, D:T.64, D:T.64, D:N.163, D:G.187, D:M.189 Water bridges: D:K.60, D:F.63 Salt bridges: D:R.46, D:K.60 COA.22: 12 residues within 4Å: Chain E: R.46, K.60, S.62, F.63, T.64, Y.137, N.163, G.165, G.166, G.187, S.188, M.189 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:R.46, E:R.46, E:S.62, E:S.62, E:T.64, E:T.64, E:N.163, E:G.187, E:M.189 Water bridges: E:K.60, E:F.63 Salt bridges: E:R.46, E:K.60 COA.27: 12 residues within 4Å: Chain F: R.46, K.60, S.62, F.63, T.64, Y.137, N.163, G.165, G.166, G.187, S.188, M.189 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:R.46, F:R.46, F:S.62, F:S.62, F:T.64, F:T.64, F:N.163, F:G.187, F:M.189 Water bridges: F:K.60, F:F.63 Salt bridges: F:R.46, F:K.60

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

ACO.3: 16 residues within 4Å: Chain A: L.731, P.732, H.733, G.734, T.939, R.955, L.961, K.991, S.994, M.1040, P.1043, I.1044, P.1045, F.1046, N.1047, R.1048 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.1043, A:P.1043, A:F.1046 Hydrogen bonds: A:G.734, A:T.939, A:T.939, A:R.955, A:S.994, A:N.1047, A:N.1047, A:R.1048 Water bridges: A:R.1048 Salt bridges: A:H.733, A:K.991, A:R.1048, A:R.1048 pi-Cation interactions: A:R.955 ACO.8: 16 residues within 4Å: Chain B: L.731, P.732, H.733, G.734, T.939, R.955, L.961, K.991, S.994, M.1040, P.1043, I.1044, P.1045, F.1046, N.1047, R.1048 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:P.1043, B:P.1043, B:F.1046 Hydrogen bonds: B:G.734, B:T.939, B:T.939, B:R.955, B:S.994, B:N.1047, B:N.1047, B:R.1048 Water bridges: B:R.1048 Salt bridges: B:H.733, B:K.991, B:R.1048, B:R.1048 pi-Cation interactions: B:R.955 ACO.13: 16 residues within 4Å: Chain C: L.731, P.732, H.733, G.734, T.939, R.955, L.961, K.991, S.994, M.1040, P.1043, I.1044, P.1045, F.1046, N.1047, R.1048 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:P.1043, C:P.1043, C:F.1046 Hydrogen bonds: C:G.734, C:T.939, C:T.939, C:R.955, C:S.994, C:N.1047, C:N.1047, C:R.1048 Water bridges: C:R.1048 Salt bridges: C:H.733, C:K.991, C:R.1048, C:R.1048 pi-Cation interactions: C:R.955 ACO.18: 16 residues within 4Å: Chain D: L.731, P.732, H.733, G.734, T.939, R.955, L.961, K.991, S.994, M.1040, P.1043, I.1044, P.1045, F.1046, N.1047, R.1048 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:P.1043, D:P.1043, D:F.1046 Hydrogen bonds: D:G.734, D:T.939, D:R.955, D:S.994, D:N.1047, D:N.1047, D:R.1048 Water bridges: D:R.1048 Salt bridges: D:H.733, D:K.991, D:R.1048, D:R.1048 pi-Cation interactions: D:R.955 ACO.23: 16 residues within 4Å: Chain E: L.731, P.732, H.733, G.734, T.939, R.955, L.961, K.991, S.994, M.1040, P.1043, I.1044, P.1045, F.1046, N.1047, R.1048 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:P.1043, E:P.1043, E:F.1046 Hydrogen bonds: E:G.734, E:T.939, E:R.955, E:S.994, E:N.1047, E:N.1047, E:R.1048 Water bridges: E:R.1048 Salt bridges: E:H.733, E:K.991, E:R.1048, E:R.1048 pi-Cation interactions: E:R.955 ACO.28: 16 residues within 4Å: Chain F: L.731, P.732, H.733, G.734, T.939, R.955, L.961, K.991, S.994, M.1040, P.1043, I.1044, P.1045, F.1046, N.1047, R.1048 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:P.1043, F:P.1043, F:F.1046 Hydrogen bonds: F:G.734, F:T.939, F:R.955, F:S.994, F:N.1047, F:N.1047, F:R.1048 Water bridges: F:R.1048 Salt bridges: F:H.733, F:K.991, F:R.1048, F:R.1048 pi-Cation interactions: F:R.955

6 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 18 residues within 4Å: Chain A: R.448, S.512, H.513, L.514, G.548, D.549, A.550, A.551, N.582, I.584, G.585, H.651 Chain E: E.805, L.851, E.853, Q.877, F.881 Ligands: MG.5 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.512, A:L.514, A:A.550, A:A.551, A:N.582 Water bridges: A:D.549, A:N.582, A:R.647 Salt bridges: A:R.448 pi-Stacking: E:F.881 TPP.9: 18 residues within 4Å: Chain B: R.448, S.512, H.513, L.514, G.548, D.549, A.550, A.551, N.582, I.584, G.585, H.651 Chain D: E.805, L.851, E.853, Q.877, F.881 Ligands: MG.10 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:S.512, B:L.514, B:A.550, B:A.551, B:N.582 Water bridges: B:D.549, B:N.582, B:R.647 Salt bridges: B:R.448 pi-Stacking: D:F.881 TPP.14: 18 residues within 4Å: Chain C: R.448, S.512, H.513, L.514, G.548, D.549, A.550, A.551, N.582, I.584, G.585, H.651 Chain F: E.805, L.851, E.853, Q.877, F.881 Ligands: MG.15 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:S.512, C:L.514, C:A.550, C:A.551, C:N.582 Water bridges: C:D.549, C:N.582, C:R.647 Salt bridges: C:R.448 pi-Stacking: F:F.881 TPP.19: 18 residues within 4Å: Chain B: E.805, L.851, E.853, Q.877, F.881 Chain D: R.448, S.512, H.513, L.514, G.548, D.549, A.550, A.551, N.582, I.584, G.585, H.651 Ligands: MG.20 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain D pi-Stacking: B:F.881 Hydrogen bonds: D:S.512, D:L.514, D:A.550, D:A.551, D:N.582, D:H.651 Water bridges: D:D.549, D:N.582, D:R.647 Salt bridges: D:R.448 TPP.24: 18 residues within 4Å: Chain A: E.805, L.851, E.853, Q.877, F.881 Chain E: R.448, S.512, H.513, L.514, G.548, D.549, A.550, A.551, N.582, I.584, G.585, H.651 Ligands: MG.25 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:S.512, E:L.514, E:A.550, E:A.551, E:N.582, E:H.651 Water bridges: E:D.549, E:N.582, E:R.647 Salt bridges: E:R.448 pi-Stacking: A:F.881 TPP.29: 18 residues within 4Å: Chain C: E.805, L.851, E.853, Q.877, F.881 Chain F: R.448, S.512, H.513, L.514, G.548, D.549, A.550, A.551, N.582, I.584, G.585, H.651 Ligands: MG.30 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain C Hydrogen bonds: F:S.512, F:L.514, F:A.550, F:A.551, F:N.582, F:H.651 Water bridges: F:D.549, F:N.582, F:R.647 Salt bridges: F:R.448 pi-Stacking: C:F.881

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.549, N.582, I.584 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.549, A:I.584, H2O.1 MG.10: 4 residues within 4Å: Chain B: D.549, N.582, I.584 Ligands: TPP.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.549, B:I.584, H2O.16 MG.15: 4 residues within 4Å: Chain C: D.549, N.582, I.584 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.549, C:I.584, H2O.31 MG.20: 4 residues within 4Å: Chain D: D.549, N.582, I.584 Ligands: TPP.19 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.549, D:I.584, H2O.46 MG.25: 4 residues within 4Å: Chain E: D.549, N.582, I.584 Ligands: TPP.24 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.549, E:I.584, H2O.62 MG.30: 4 residues within 4Å: Chain F: D.549, N.582, I.584 Ligands: TPP.29 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.549, F:I.584, H2O.77

Links

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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
A

C
A

D
A

E
A

F
A

2-oxoglutarate dehydrogenase E1/E2 component