SMTL ID : 7npf.1

Vibrio cholerae ParA2-ATPyS-DNA filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.125, D.151, P.260 Ligands: AGS.2 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain B: N.114, V.115, Q.116, T.258 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.115, B:T.258 MG.5: 4 residues within 4Å: Chain C: S.125, D.151, P.260 Ligands: AGS.6 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: N.114, V.115, Q.116, T.258 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:V.115, D:T.258 MG.9: 4 residues within 4Å: Chain E: S.125, D.151, P.260 Ligands: AGS.10 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain F: N.114, V.115, Q.116, T.258 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:V.115, F:T.258 MG.13: 4 residues within 4Å: Chain G: S.125, D.151, P.260 Ligands: AGS.14 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain H: N.114, V.115, Q.116, T.258 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:V.115, H:T.258

8 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Covalent)(Non-covalent)

AGS.2: 19 residues within 4Å: Chain A: K.119, G.120, G.121, T.122, G.123, K.124, S.125, M.126, P.260, P.349, R.350, S.351, F.354, E.355 Chain B: K.119, K.283, L.285, D.286 Ligands: MG.1 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.121, A:T.122, A:G.123, A:K.124, A:S.125, A:M.126, A:P.349, B:D.286, B:D.286 Salt bridges: A:K.124, B:K.119, B:K.119 AGS.4: 17 residues within 4Å: Chain A: K.119, G.120, K.283, L.285 Chain B: G.120, G.121, T.122, G.123, K.124, S.125, M.126, D.151, P.260, M.320, F.354, E.355, A.358 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.121, B:T.122, B:G.123, B:K.124, B:S.125, B:M.126, B:D.151, B:D.151, A:K.119 Salt bridges: A:K.119 AGS.6: 19 residues within 4Å: Chain C: K.119, G.120, G.121, T.122, G.123, K.124, S.125, M.126, P.260, P.349, R.350, S.351, F.354, E.355 Chain D: K.119, K.283, L.285, D.286 Ligands: MG.5 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain C Hydrogen bonds: D:D.286, D:D.286, C:G.121, C:T.122, C:G.123, C:K.124, C:S.125, C:M.126, C:P.349 Salt bridges: D:K.119, D:K.119, C:K.124 AGS.8: 17 residues within 4Å: Chain C: K.119, G.120, K.283, L.285 Chain D: G.120, G.121, T.122, G.123, K.124, S.125, M.126, D.151, P.260, M.320, F.354, E.355, A.358 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:K.119, C:G.120, D:G.121, D:T.122, D:G.123, D:K.124, D:S.125, D:M.126, D:D.151, D:D.151 Salt bridges: C:K.119 AGS.10: 19 residues within 4Å: Chain E: K.119, G.120, G.121, T.122, G.123, K.124, S.125, M.126, P.260, P.349, R.350, S.351, F.354, E.355 Chain F: K.119, K.283, L.285, D.286 Ligands: MG.9 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.121, E:T.122, E:G.123, E:K.124, E:S.125, E:M.126, E:P.349, F:D.286, F:D.286 Salt bridges: E:K.124, F:K.119, F:K.119 AGS.12: 17 residues within 4Å: Chain E: K.119, G.120, K.283, L.285 Chain F: G.120, G.121, T.122, G.123, K.124, S.125, M.126, D.151, P.260, M.320, F.354, E.355, A.358 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.121, F:T.122, F:G.123, F:K.124, F:S.125, F:M.126, F:D.151, F:D.151, E:K.119 Salt bridges: E:K.119 AGS.14: 19 residues within 4Å: Chain G: K.119, G.120, G.121, T.122, G.123, K.124, S.125, M.126, P.260, P.349, R.350, S.351, F.354, E.355 Chain H: K.119, K.283, L.285, D.286 Ligands: MG.13 12 PLIP interactions: 8 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:G.121, G:T.122, G:G.123, G:K.124, G:S.125, G:M.126, G:P.349, H:D.286, H:D.286 Salt bridges: G:K.124, H:K.119, H:K.119 AGS.16: 17 residues within 4Å: Chain G: K.119, G.120, K.283, L.285 Chain H: G.120, G.121, T.122, G.123, K.124, S.125, M.126, D.151, P.260, M.320, F.354, E.355, A.358 10 PLIP interactions: 8 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:G.121, H:T.122, H:G.123, H:K.124, H:S.125, H:M.126, H:D.151, H:D.151, G:K.119 Salt bridges: G:K.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parker, A.V. et al., The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding. Nat Commun (2021)

Release Date

2021-10-06

Peptides

AAA family ATPase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

AAA family ATPase

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