SMTL ID : 9dls.1

Vibrio cholerae DnaB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.37 Å

Oligo State

homo-hexamer

Ligands

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

AGS.1: 19 residues within 4Å: Chain A: P.230, S.231, M.232, G.233, K.234, T.235, T.236, E.259, R.268, Q.278, R.282, Q.381, R.417, F.450, G.452 Chain F: K.437, P.442, I.443 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.231, A:M.232, A:G.233, A:K.234, A:T.235, A:T.236, A:T.236, A:E.259, A:R.268, A:R.282, A:R.282, A:R.417, A:R.417 Salt bridges: A:R.268 AGS.3: 12 residues within 4Å: Chain B: P.230, S.231, M.232, G.233, K.234, T.235, T.236, E.259, Q.278, T.279, G.452 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.231, B:S.231, B:S.231, B:M.232, B:G.233, B:T.235, B:T.235, B:T.236, B:E.259, B:T.279, B:T.279, B:R.417 Salt bridges: B:R.268 AGS.5: 18 residues within 4Å: Chain B: K.437, Q.438, R.439, G.441 Chain C: S.231, G.233, K.234, T.235, T.236, E.259, R.268, Q.278, T.279, Q.381, F.450, G.452, H.453 Ligands: MG.6 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.231, C:G.233, C:K.234, C:T.235, C:T.236, C:E.259, C:D.277, C:T.279, B:K.437, B:R.439 Salt bridges: C:R.268 AGS.7: 22 residues within 4Å: Chain C: Q.407, K.437, Q.438, R.439, N.440, G.441 Chain D: S.231, G.233, K.234, T.235, T.236, E.259, R.268, D.277, Q.278, T.279, Q.381, R.417, F.450, G.452, H.453 Ligands: MG.8 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:S.231, D:S.231, D:M.232, D:G.233, D:K.234, D:T.235, D:T.235, D:T.236, D:T.279, D:R.417, C:Q.407, C:K.437, C:Q.438, C:R.439, C:R.439 Salt bridges: D:K.234, D:R.268 AGS.9: 22 residues within 4Å: Chain D: Q.407, K.437, Q.438, R.439, N.440, G.441, P.442 Chain E: S.231, M.232, G.233, K.234, T.235, T.236, E.259, R.268, D.277, Q.278, T.279, Q.381, G.452, H.453 Ligands: MG.10 14 PLIP interactions: 11 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.231, E:M.232, E:G.233, E:K.234, E:T.235, E:T.236, E:T.236, E:E.259, E:D.277, E:Q.278, D:Q.407, D:K.437, D:R.439 Salt bridges: E:R.268 AGS.11: 22 residues within 4Å: Chain E: K.437, Q.438, R.439, N.440, G.441 Chain F: P.230, S.231, M.232, G.233, K.234, T.235, T.236, E.259, R.268, D.277, Q.278, T.279, Q.381, R.417, G.452, H.453 Ligands: MG.12 16 PLIP interactions: 3 interactions with chain E, 13 interactions with chain F Hydrogen bonds: E:K.437, E:Q.438, E:R.439, F:S.231, F:S.231, F:M.232, F:G.233, F:K.234, F:T.235, F:T.236, F:T.236, F:E.259, F:E.259, F:D.277, F:R.417 Salt bridges: F:R.268

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.235, E.259, D.340 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.235 MG.4: 4 residues within 4Å: Chain B: T.235, D.340, L.379 Ligands: AGS.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.235, B:D.340, B:D.340 MG.6: 4 residues within 4Å: Chain C: T.235, E.259, D.340 Ligands: AGS.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.235, C:E.259 MG.8: 4 residues within 4Å: Chain D: T.235, E.259, D.340 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.235, D:E.259 MG.10: 4 residues within 4Å: Chain E: T.235, E.259, D.340 Ligands: AGS.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.235, E:E.259 MG.12: 4 residues within 4Å: Chain F: T.235, E.259, D.340 Ligands: AGS.11 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.235, F:E.259, F:E.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, N. et al., DnaB and DciA: mechanisms of helicase loading and translocation on ssDNA. Nucleic Acids Res. (2025)

Release Date

2025-07-16

Peptides

Replicative DNA helicase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Replicative DNA helicase