SMTL ID : 8ys5.1

Cryo-EM structure of the Helicobacter pylori OorDABC complex in the apo-form

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

6 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 10 residues within 4Å: Chain A: C.19, K.20, G.21, C.22, D.23, C.25, M.36, C.66, D.68, A.70 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.68 Metal complexes: A:C.19, A:C.22, A:C.25, A:C.66 SF4.2: 9 residues within 4Å: Chain A: V.28, C.29, P.30, A.31, L.34, C.56, I.57, C.59, C.62 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:C.29, A:C.56, A:C.59, A:C.59, A:C.62 SF4.3: 10 residues within 4Å: Chain C: W.18, C.19, C.22, C.53, N.123, G.127, C.202, N.205 Chain D: V.43 Ligands: TPP.5 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.19, C:C.22, C:C.53, C:C.202 SF4.6: 9 residues within 4Å: Chain E: C.19, K.20, G.21, C.22, C.25, M.36, H.65, C.66, D.68 5 PLIP interactions: 5 interactions with chain E, Salt bridges: E:D.68 Metal complexes: E:C.19, E:C.22, E:C.25, E:C.66 SF4.7: 11 residues within 4Å: Chain E: V.12, C.29, P.30, V.33, L.34, S.55, C.56, I.57, C.59, C.62, V.73 5 PLIP interactions: 5 interactions with chain E, Metal complexes: E:C.29, E:C.56, E:C.59, E:C.59, E:C.62 SF4.8: 9 residues within 4Å: Chain G: W.18, C.19, C.22, C.53, N.123, G.127, C.202, N.205 Chain H: V.43 5 PLIP interactions: 5 interactions with chain G, Salt bridges: G:D.24 Metal complexes: G:C.19, G:C.22, G:C.53, G:C.202

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain C: D.95, N.123, I.125 Ligands: TPP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.95 MG.9: 4 residues within 4Å: Chain G: D.95, N.123, I.125 Ligands: TPP.10 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.95, G:I.125

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.5: 19 residues within 4Å: Chain B: P.28, I.29, R.106, T.111 Chain C: I.51, G.52, C.53, S.54, D.95, G.96, D.97, N.123, I.125, Y.126, G.127, L.128, T.129 Ligands: SF4.3, MG.4 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.51, C:Y.126, B:I.29, B:T.111 Hydrogen bonds: C:C.53, C:S.54, C:G.96, C:D.97, C:D.97, C:N.123, C:N.123, C:G.127, C:L.128, B:R.106, B:R.106 pi-Cation interactions: C:H.70 TPP.10: 20 residues within 4Å: Chain F: P.28, T.30, R.106, T.111 Chain G: I.51, G.52, C.53, S.54, H.70, G.94, D.95, G.96, D.97, N.123, I.125, Y.126, G.127, L.128, T.129 Ligands: MG.9 14 PLIP interactions: 10 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:I.51, G:Y.126, F:T.111 Hydrogen bonds: G:C.53, G:S.54, G:G.96, G:D.97, G:D.97, G:I.125, G:G.127, G:L.128, F:T.30, F:R.106, F:R.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lan, W. et al., Cryo-EM structure of the Helicobacter pylori OorDABC complex in the apo-form. To Be Published

Release Date

2025-07-02

Peptides

2-oxoglutarate:acceptor oxidoreductase: AE
2-oxoglutarate synthase subunit alpha: BF
2-oxoglutarate ferredoxin oxidoreductase subunit beta: CG
2-oxoglutarate:acceptor oxidoreductase: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

E
F

B
A

F
G

C
C

G
H

D
B

H
I

2-oxoglutarate:acceptor oxidoreductase

2-oxoglutarate synthase subunit alpha

2-oxoglutarate ferredoxin oxidoreductase subunit beta

2-oxoglutarate:acceptor oxidoreductase

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