SMTL ID : 9oa1.1

Ecoli DnaB helicase and Phage Lambda loader P with ADP-Mg in a 6:5 stoichiometry ratio.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-5-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: S.234, M.235, G.236, K.237, T.238, T.239, R.271, Q.281, T.282, R.420, G.455 Chain F: R.442, N.443, G.444 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.234, A:S.234, A:M.235, A:G.236, A:K.237, A:T.238, A:T.238, A:T.239, A:T.282, A:R.420 Salt bridges: A:K.237, A:R.271 ADP.3: 15 residues within 4Å: Chain B: S.234, M.235, G.236, K.237, T.238, T.239, R.271, Q.281, R.285, R.420, F.453, G.455, Q.456 Chain K: Y.27 Ligands: MG.4 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain K Hydrogen bonds: B:S.234, B:S.234, B:M.235, B:G.236, B:K.237, B:T.238, B:T.239, B:Q.281, B:R.285, B:R.285, B:R.420 Salt bridges: B:R.271 pi-Stacking: K:Y.27 ADP.5: 15 residues within 4Å: Chain B: R.442, G.444 Chain C: S.234, M.235, G.236, K.237, T.238, T.239, R.271, Q.281, T.282, R.420, G.455, Q.456 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.234, C:S.234, C:M.235, C:G.236, C:K.237, C:T.238, C:T.238, C:T.239, C:T.282, C:R.420 Salt bridges: C:K.237, C:R.271 ADP.7: 14 residues within 4Å: Chain C: R.442 Chain D: S.234, M.235, G.236, K.237, T.238, T.239, R.271, Q.281, T.282, R.420, G.455, Q.456 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.232, D:S.234, D:S.234, D:M.235, D:G.236, D:K.237, D:T.238, D:T.238, D:T.239, D:T.282, D:R.420 Salt bridges: D:K.237, D:R.271 ADP.9: 15 residues within 4Å: Chain D: R.442, N.443, G.444 Chain E: S.234, M.235, G.236, K.237, T.238, T.239, R.271, T.282, R.285, R.420, G.455 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:S.234, E:S.234, E:M.235, E:G.236, E:K.237, E:T.238, E:T.238, E:T.239, E:T.282, E:R.285, E:R.420, E:R.420 Salt bridges: E:K.237, E:R.271 ADP.11: 14 residues within 4Å: Chain E: R.442 Chain F: S.234, M.235, G.236, K.237, T.238, T.239, R.271, Q.281, T.282, R.420, G.455, Q.456 Ligands: MG.12 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:S.234, F:S.234, F:M.235, F:G.236, F:K.237, F:T.238, F:T.238, F:T.239, F:T.282, F:R.420 Salt bridges: F:K.237, F:R.271, E:R.442

6 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shatarupa, A. et al., Distinct Quaternary States, Intermediates, and Autoinhibition During Loading of the DnaB-Replicative Helicase by the Phage lambda P Helicase Loader. Biorxiv (2025)

Release Date

2025-07-16

Peptides

Replicative DNA helicase: ABCDEF
Helicase loader: GHIJK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
V

H
W

I
X

J
Y

K
Z

Replicative DNA helicase

Helicase loader

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