SMTL ID : 9e26.1

Compact structure of CpaF with two ATPs and two ADPs (Under-saturated ATP/ADP dataset)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.288, E.357 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.288 MG.4: 3 residues within 4Å: Chain B: T.288, E.357 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.288 MG.5: 4 residues within 4Å: Chain D: T.288, E.312, E.357 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.288 MG.7: 3 residues within 4Å: Chain E: T.288, E.357 Ligands: ADP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.288

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 17 residues within 4Å: Chain A: R.217, K.244, L.248, L.253, F.256, S.258, T.283, G.284, S.285, G.286, K.287, T.288, T.289, E.312, R.431 Chain F: R.347 Ligands: MG.1 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:R.217, A:S.258, A:S.258, A:T.283, A:G.284, A:S.285, A:G.286, A:G.286, A:K.287, A:T.288, A:T.289, A:T.289, A:E.312, A:R.431 Salt bridges: A:K.287, A:K.287, F:R.347 ATP.6: 17 residues within 4Å: Chain C: R.347 Chain D: R.217, K.244, L.248, L.253, F.256, S.258, T.283, G.284, S.285, G.286, K.287, T.288, T.289, E.312, R.431 Ligands: MG.5 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.217, D:S.258, D:S.258, D:G.284, D:S.285, D:G.286, D:G.286, D:K.287, D:T.288, D:T.289, D:T.289, D:R.431 Salt bridges: D:K.287, D:K.287, C:R.347

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

ADP.3: 13 residues within 4Å: Chain B: K.244, L.248, L.253, F.256, S.258, G.284, S.285, G.286, K.287, T.288, T.289, R.431 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.244, B:S.258, B:S.258, B:G.284, B:S.285, B:G.286, B:K.287, B:T.288, B:T.289, B:T.289, B:R.431 Salt bridges: B:K.287 pi-Cation interactions: B:R.431 ADP.8: 13 residues within 4Å: Chain E: K.244, L.248, L.253, F.256, S.258, G.284, S.285, G.286, K.287, T.288, T.289, R.431 Ligands: MG.7 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:K.244, E:K.244, E:S.258, E:S.258, E:G.284, E:S.285, E:G.286, E:K.287, E:T.288, E:T.289, E:T.289, E:R.431 Salt bridges: E:K.287 pi-Cation interactions: E:R.431

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yen, I.Y. et al., Conformational changes in the motor ATPase CpaF facilitate a rotary mechanism of Tad pilus assembly. Nat Commun (2025)

Release Date

2025-04-23

Peptides

CpaF: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

CpaF

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