SMTL ID : 8dzg.1

Cryo-EM structure of bundle-forming pilus extension ATPase from E.coli in the presence of ADP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.267, E.295 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.267 MG.4: 3 residues within 4Å: Chain B: S.267, E.295 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.267 MG.7: 3 residues within 4Å: Chain C: S.267, E.295 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.267 MG.10: 3 residues within 4Å: Chain D: S.267, E.295 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.267 MG.13: 3 residues within 4Å: Chain E: S.267, E.295 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.267 MG.16: 3 residues within 4Å: Chain F: S.267, E.295 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.267

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 13 residues within 4Å: Chain A: F.235, T.262, G.263, S.264, G.265, K.266, S.267, T.268, Y.296, L.398, R.453, I.455 Ligands: MG.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.235, A:K.266, A:S.267, A:T.268, A:T.268 ADP.5: 13 residues within 4Å: Chain B: F.235, T.262, G.263, S.264, G.265, K.266, S.267, T.268, Y.296, L.398, R.453, I.455 Ligands: MG.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.235, B:K.266, B:S.267, B:T.268, B:T.268 ADP.8: 13 residues within 4Å: Chain C: F.235, T.262, G.263, S.264, G.265, K.266, S.267, T.268, Y.296, L.398, R.453, I.455 Ligands: MG.7 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.235, C:K.266, C:S.267, C:T.268, C:T.268 ADP.11: 13 residues within 4Å: Chain D: F.235, T.262, G.263, S.264, G.265, K.266, S.267, T.268, Y.296, L.398, R.453, I.455 Ligands: MG.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:F.235, D:K.266, D:S.267, D:T.268, D:T.268 ADP.14: 13 residues within 4Å: Chain E: F.235, T.262, G.263, S.264, G.265, K.266, S.267, T.268, Y.296, L.398, R.453, I.455 Ligands: MG.13 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:F.235, E:K.266, E:S.267, E:T.268, E:T.268 ADP.17: 13 residues within 4Å: Chain F: F.235, T.262, G.263, S.264, G.265, K.266, S.267, T.268, Y.296, L.398, R.453, I.455 Ligands: MG.16 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:F.235, F:K.266, F:S.267, F:T.268, F:T.268

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.403, C.406, C.445, C.446 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.403, A:C.406, A:C.445, A:C.446 ZN.6: 4 residues within 4Å: Chain B: C.403, C.406, C.445, C.446 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.403, B:C.406, B:C.445, B:C.446 ZN.9: 4 residues within 4Å: Chain C: C.403, C.406, C.445, C.446 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.403, C:C.406, C:C.445, C:C.446 ZN.12: 4 residues within 4Å: Chain D: C.403, C.406, C.445, C.446 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.403, D:C.406, D:C.445, D:C.446 ZN.15: 4 residues within 4Å: Chain E: C.403, C.406, C.445, C.446 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.403, E:C.406, E:C.445, E:C.446 ZN.18: 4 residues within 4Å: Chain F: C.403, C.406, C.445, C.446 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.403, F:C.406, F:C.445, F:C.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nayak, A.R. et al., Cryo-EM Structure of the Type IV Pilus Extension ATPase from Enteropathogenic Escherichia coli. Mbio (2022)

Release Date

2022-10-26

Peptides

BfpD: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

BfpD

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