SMTL ID : 6t66.1

Crystal structure of the Vibrio cholerae replicative helicase (DnaB) with GDP-AlF4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.90 Å

Oligo State

homo-hexamer

Ligands

6 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: P.230, S.231, M.232, G.233, K.234, T.235, T.236, R.268, Q.278, T.279, R.417, G.452, H.453 Chain B: Q.438, R.439, N.440, G.441, P.442 Ligands: MG.2, ALF.3 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.231, A:S.231, A:M.232, A:G.233, A:K.234, A:T.235, A:T.236, A:T.236, A:T.279, A:R.417, B:Q.438 Salt bridges: A:K.234, A:R.268, B:K.437 GDP.4: 20 residues within 4Å: Chain B: P.230, S.231, M.232, G.233, K.234, T.235, T.236, R.268, Q.278, T.279, R.417, G.452, H.453 Chain C: Q.438, R.439, N.440, G.441, P.442 Ligands: MG.5, ALF.6 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.231, B:S.231, B:M.232, B:G.233, B:K.234, B:T.235, B:T.236, B:T.236, B:T.279, B:R.417, C:Q.438 Salt bridges: B:K.234, B:R.268 GDP.7: 20 residues within 4Å: Chain C: P.230, S.231, M.232, G.233, K.234, T.235, T.236, R.268, Q.278, T.279, R.417, G.452, H.453 Chain D: Q.438, R.439, N.440, G.441, P.442 Ligands: MG.8, ALF.9 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.229, C:S.231, C:S.231, C:M.232, C:G.233, C:K.234, C:T.235, C:T.235, C:T.236, C:T.236, C:T.279, C:R.417, C:H.453, D:Q.438 Salt bridges: C:K.234, C:R.268, D:K.437 GDP.10: 15 residues within 4Å: Chain D: P.230, S.231, M.232, G.233, K.234, T.235, T.236, R.268, Q.278, T.279, R.417, G.452, H.453 Ligands: MG.11, ALF.12 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:R.229, 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.236, D:T.279, D:R.417, D:H.453 Salt bridges: D:K.234, D:R.268 GDP.13: 20 residues within 4Å: Chain E: P.230, S.231, M.232, G.233, K.234, T.235, T.236, R.268, Q.278, T.279, R.417, G.452, H.453 Chain F: Q.438, R.439, N.440, G.441, P.442 Ligands: MG.14, ALF.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.231, E:S.231, E:M.232, E:G.233, E:K.234, E:T.235, E:T.235, E:T.236, E:T.236, E:T.279, E:R.417, E:H.453 Salt bridges: E:K.234, E:R.268 GDP.16: 15 residues within 4Å: Chain F: P.230, S.231, M.232, G.233, K.234, T.235, T.236, R.268, Q.278, T.279, R.417, G.452, H.453 Ligands: MG.17, ALF.18 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: 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:T.279, F:R.417 Salt bridges: F:K.234, F:R.268

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.235, E.259, M.260, D.340 Ligands: GDP.1, ALF.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.235 MG.5: 6 residues within 4Å: Chain B: T.235, E.259, M.260, D.340 Ligands: GDP.4, ALF.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.235 MG.8: 6 residues within 4Å: Chain C: T.235, E.259, M.260, D.340 Ligands: GDP.7, ALF.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.235 MG.11: 6 residues within 4Å: Chain D: T.235, E.259, M.260, D.340 Ligands: GDP.10, ALF.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.235 MG.14: 6 residues within 4Å: Chain E: T.235, E.259, M.260, D.340 Ligands: GDP.13, ALF.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.235 MG.17: 6 residues within 4Å: Chain F: T.235, E.259, M.260, D.340 Ligands: GDP.16, ALF.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.235

6 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 11 residues within 4Å: Chain A: P.230, S.231, K.234, E.259, Y.341, Q.381 Chain B: E.406, K.437, R.439 Ligands: GDP.1, MG.2 No protein-ligand interaction detected (PLIP) ALF.6: 12 residues within 4Å: Chain B: P.230, S.231, K.234, E.259, Y.341, Q.381 Chain C: E.406, Q.407, K.437, R.439 Ligands: GDP.4, MG.5 No protein-ligand interaction detected (PLIP) ALF.9: 12 residues within 4Å: Chain C: P.230, S.231, K.234, E.259, Y.341, Q.381 Chain D: E.406, Q.407, K.437, R.439 Ligands: GDP.7, MG.8 No protein-ligand interaction detected (PLIP) ALF.12: 8 residues within 4Å: Chain D: P.230, S.231, K.234, E.259, Y.341, Q.381 Ligands: GDP.10, MG.11 No protein-ligand interaction detected (PLIP) ALF.15: 11 residues within 4Å: Chain E: P.230, S.231, K.234, E.259, Y.341, Q.381 Chain F: E.406, K.437, R.439 Ligands: GDP.13, MG.14 No protein-ligand interaction detected (PLIP) ALF.18: 8 residues within 4Å: Chain F: P.230, S.231, K.234, E.259, Y.341, Q.381 Ligands: GDP.16, MG.17 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marsin, S. et al., Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase. Nucleic Acids Res. (2021)

Release Date

2021-04-28

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

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