SMTL ID : 8ys6.1

Helicobacter pylori OorDABC in complex with Napabucasin

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: 12 residues within 4Å: Chain A: C.19, K.20, G.21, C.22, D.23, C.25, M.36, A.48, C.66, P.67, 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: 8 residues within 4Å: Chain A: C.29, V.33, L.34, C.56, I.57, C.59, C.62, V.73 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 SF4.4: 8 residues within 4Å: Chain C: W.18, C.19, C.22, C.53, N.123, C.202, N.205 Chain D: V.43 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.19, C:C.22, C:C.53, C:C.202 SF4.7: 11 residues within 4Å: Chain E: C.19, K.20, G.21, C.22, D.23, C.25, M.36, A.48, H.65, C.66, D.68 4 PLIP interactions: 4 interactions with chain E, Salt bridges: E:D.68 Metal complexes: E:C.22, E:C.25, E:C.66 SF4.8: 9 residues within 4Å: Chain E: C.29, A.31, V.33, L.34, C.56, I.57, C.59, C.62, V.73 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:I.57, E:C.59, E:C.62 SF4.10: 8 residues within 4Å: Chain G: W.18, C.19, C.22, C.53, N.123, G.127, C.202, N.205 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 01: 2-ethanoylbenzo[f][1]benzofuran-4,9-dione

01.3: 5 residues within 4Å: Chain A: L.44, K.46 Chain C: W.20 Chain D: G.12, R.44 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.44, C:W.20 Hydrogen bonds: A:K.46 pi-Stacking: C:W.20 01.9: 6 residues within 4Å: Chain E: L.44, K.46 Chain G: W.20 Chain H: G.12, R.44, K.122 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: G:W.20 pi-Stacking: G:W.20 Hydrogen bonds: E:K.46

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain C: D.95, N.123, I.125 Ligands: TPP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.95, C:I.125 MG.11: 4 residues within 4Å: Chain G: D.95, N.123, I.125 Ligands: TPP.12 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.95, G:I.125

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.6: 21 residues within 4Å: Chain B: P.28, I.29, P.80, R.106, T.111 Chain C: 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.5 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.126, C:T.129, B:P.80 Hydrogen bonds: C:C.53, C:S.54, C:S.54, C:D.95, C:G.96, C:D.97, C:D.97, C:N.123, C:G.127, C:L.128, B:R.106 pi-Stacking: C:H.70 TPP.12: 21 residues within 4Å: Chain B: E.87 Chain F: P.28, I.29, P.80, R.106, T.111 Chain G: 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.11 14 PLIP interactions: 11 interactions with chain G, 3 interactions with chain F Hydrophobic interactions: G:H.70, F:I.29, F:P.80 Hydrogen bonds: G:C.53, G:S.54, G:H.70, G:G.94, G:G.96, G:D.97, G:N.123, G:G.127, G:L.128, F:R.106 pi-Stacking: G:H.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lan, W. et al., Helicobacter pylori OorDABC in complex with Napabucasin. 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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