SMTL ID : 9eco.1

E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-mer

Ligands

5 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.1: 12 residues within 4Å: Chain A: E.409, Q.410, K.440, R.442 Chain B: P.233, S.234, K.237, E.262, Y.344, Q.384 Ligands: ADP.2, MG.3 No protein-ligand interaction detected (PLIP) ALF.5: 10 residues within 4Å: Chain B: Q.410, K.440, R.442 Chain C: P.233, S.234, K.237, E.262, Q.384 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP) ALF.7: 10 residues within 4Å: Chain C: Q.410, K.440, R.442 Chain D: P.233, S.234, K.237, E.262, Q.384 Ligands: ADP.8, MG.9 No protein-ligand interaction detected (PLIP) ALF.11: 10 residues within 4Å: Chain D: Q.410, K.440, R.442 Chain E: P.233, S.234, K.237, E.262, Q.384 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP) ALF.14: 10 residues within 4Å: Chain E: Q.410, K.440, R.442 Chain F: P.233, S.234, K.237, E.262, Q.384 Ligands: ADP.13, MG.15 No protein-ligand interaction detected (PLIP)

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

ADP.2: 24 residues within 4Å: Chain A: Q.441, R.442, N.443, G.444, P.445, I.446 Chain B: P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, D.280, Q.281, T.282, R.285, R.420, F.453, G.455, Q.456 Ligands: ALF.1, MG.3 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.234, B:S.234, B:M.235, B:G.236, B:K.237, B:T.238, B:T.239, B:T.282, A:Q.441, A:G.444 Salt bridges: B:K.237, B:R.271 ADP.4: 23 residues within 4Å: Chain B: Q.441, R.442, N.443, G.444, P.445, I.446 Chain C: P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, D.280, Q.281, T.282, R.420, F.453, G.455, Q.456 Ligands: ALF.5, MG.6 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.234, C:S.234, C:M.235, C:G.236, C:K.237, C:T.238, C:T.239, C:T.239, C:T.282, B:Q.441, B:G.444 Salt bridges: C:K.237, C:R.271 ADP.8: 23 residues within 4Å: Chain C: Q.441, R.442, N.443, G.444, P.445, I.446 Chain D: P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, D.280, Q.281, T.282, R.420, F.453, G.455, Q.456 Ligands: ALF.7, MG.9 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:S.234, D:M.235, D:G.236, D:K.237, D:T.238, D:T.239, D:T.239, D:T.282, D:R.420, C:Q.441, C:G.444 Salt bridges: D:R.271 ADP.10: 22 residues within 4Å: Chain D: Q.441, R.442, N.443, G.444, P.445, I.446 Chain E: P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, Q.281, T.282, R.420, F.453, G.455, Q.456 Ligands: ALF.11, MG.12 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:S.234, E:S.234, E:S.234, E:M.235, E:G.236, E:K.237, E:T.238, E:T.239, E:T.282, E:R.420, D:Q.441, D:G.444 Salt bridges: E:K.237, E:R.271 ADP.13: 23 residues within 4Å: Chain E: Q.441, R.442, N.443, G.444, P.445, I.446 Chain F: P.233, S.234, M.235, G.236, K.237, T.238, T.239, R.271, D.280, Q.281, T.282, R.420, F.453, G.455, Q.456 Ligands: ALF.14, MG.15 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.234, F:S.234, F:S.234, F:M.235, F:G.236, F:K.237, F:T.238, F:T.239, E:Q.441 Salt bridges: F:K.237, F:R.271

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: R.442 Chain B: T.238, E.262, D.343 Ligands: ALF.1, ADP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.238 MG.6: 4 residues within 4Å: Chain C: T.238, E.262 Ligands: ADP.4, ALF.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.238 MG.9: 5 residues within 4Å: Chain C: R.442 Chain D: T.238, E.262 Ligands: ALF.7, ADP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.238 MG.12: 4 residues within 4Å: Chain E: T.238, E.262 Ligands: ADP.10, ALF.11 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.238 MG.15: 5 residues within 4Å: Chain F: T.238, E.262, D.343 Ligands: ADP.13, ALF.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oakley, A.J. et al., Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli. To Be Published

Release Date

2024-12-11

Peptides

Replicative DNA helicase: ABCDEF
DNA primase: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Replicative DNA helicase

DNA primase

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