SMTL ID : 7t20.1

E. coli DnaB bound to ssDNA and AMPPNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 25 residues within 4Å: Chain B: Q.410, K.440, Q.441, R.442, G.444, P.445 Chain C: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, M.263, R.271, D.280, Q.281, T.282, Q.384, R.420, G.455, Q.456 Ligands: MG.2 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.234, 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.239, C:D.280, C:T.282, C:T.282, C:Q.384, C:R.420, C:S.458, B:K.440, B:K.440, B:G.444 Salt bridges: C:R.271 ANP.3: 24 residues within 4Å: Chain C: K.440, Q.441, R.442, N.443, G.444, P.445 Chain D: P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, M.263, R.271, D.280, Q.281, T.282, Q.384, G.455, Q.456, S.458 Ligands: MG.4 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:S.234, D:M.235, D:G.236, D:K.237, D:K.237, D:K.237, D:T.238, D:T.239, D:E.262, D:R.271, D:D.280, D:T.282, D:T.282, D:Q.384, D:S.458, C:K.440, C:Q.441, C:G.444 Salt bridges: D:R.271 ANP.5: 26 residues within 4Å: Chain D: K.440, Q.441, R.442, N.443, G.444, P.445 Chain E: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, R.271, D.280, Q.281, T.282, Q.384, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.6 19 PLIP interactions: 17 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:K.237, E:K.237, E:T.238, E:T.239, E:D.280, E:Q.281, E:T.282, E:Q.384, E:R.420, E:S.458, D:K.440, D:G.444 Salt bridges: E:R.271 ANP.7: 26 residues within 4Å: Chain E: K.440, R.442, G.444, P.445, I.446 Chain F: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, M.263, R.271, D.280, Q.281, T.282, Q.384, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.8 18 PLIP interactions: 3 interactions with chain E, 15 interactions with chain F Hydrogen bonds: E:K.440, E:G.444, E:I.446, F:S.234, F:S.234, F:M.235, F:G.236, F:K.237, F:K.237, F:T.238, F:T.239, F:T.239, F:D.280, F:T.282, F:Q.384, F:R.420, F:S.458 Salt bridges: F:R.271

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain C: K.237, T.238, E.262 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.238 MG.4: 5 residues within 4Å: Chain D: K.237, T.238, E.262, D.343 Ligands: ANP.3 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.238, D:E.262 MG.6: 4 residues within 4Å: Chain E: K.237, T.238, E.262 Ligands: ANP.5 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.238, E:E.262 MG.8: 5 residues within 4Å: Chain F: K.237, T.238, E.262, D.343 Ligands: ANP.7 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.238, F:E.262

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

2022-12-14

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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