SMTL ID : 9e29.1

Expanded structure of CpaF with two ATPs and four ADPs (Saturated ATP dataset)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.288, E.312, E.357 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.288, A:E.312 MG.3: 4 residues within 4Å: Chain B: K.287, T.288, E.312 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain C: T.288, E.312 Ligands: ADP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.288, C:E.312 MG.7: 4 residues within 4Å: Chain D: T.288, E.312, E.357 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.288, D:E.312 MG.10: 4 residues within 4Å: Chain E: K.287, T.288, E.312 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.288 MG.12: 3 residues within 4Å: Chain F: T.288, E.312 Ligands: ADP.11 No protein-ligand interaction detected (PLIP)

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

ATP.2: 18 residues within 4Å: Chain A: R.223, 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, E.357, R.431 Chain F: R.347 Ligands: MG.1 16 PLIP interactions: 1 interactions with chain F, 15 interactions with chain A Salt bridges: F:R.347, A:R.223, A:K.287, A:K.287 Hydrogen bonds: A:K.244, A:S.258, A:S.258, A:G.284, A:G.286, A:G.286, A:K.287, A:T.288, A:T.289, A:T.289, A:E.357 pi-Cation interactions: A:R.431 ATP.8: 15 residues within 4Å: Chain C: R.347 Chain D: R.223, L.248, L.253, F.256, S.258, T.283, G.284, S.285, G.286, K.287, T.288, T.289, R.431 Ligands: MG.7 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.244, D:K.244, D:S.258, D:S.258, D:G.284, D:S.285, D:G.286, D:K.287, D:T.288, D:T.289, D:T.289 Salt bridges: D:R.223, D:K.287, D:K.287, C:R.347

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

ADP.4: 15 residues within 4Å: Chain B: K.244, L.248, L.253, F.256, S.258, G.282, T.283, G.284, S.285, G.286, K.287, T.288, T.289, R.431 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:K.244, 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 Salt bridges: B:K.287 pi-Cation interactions: B:R.431 ADP.6: 13 residues within 4Å: Chain C: 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.5 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.244, C:K.244, C:S.258, C:S.258, C:G.284, C:G.286, C:K.287, C:T.288, C:T.288, C:T.289, C:T.289, C:R.431 Salt bridges: C:K.244, C:K.287 ADP.9: 14 residues within 4Å: Chain E: K.244, L.248, F.256, S.258, T.283, G.284, S.285, G.286, K.287, T.288, T.289, E.312, R.431 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:K.244, E:K.244, E:S.258, E:S.258, E:G.284, E:G.286, E:T.288, E:T.288 Salt bridges: E:K.287, E:K.287 pi-Cation interactions: E:R.431 ADP.11: 13 residues within 4Å: Chain F: 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.12 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:K.244, F:K.244, F:S.258, F:S.258, F:G.284, F:G.286, F:K.287, F:T.288, F:T.288, F:T.289 Salt bridges: F:K.244, F:K.287

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

Related Entries With Identical Sequence