SMTL ID : 4nmn.1

Aquifex aeolicus replicative helicase (DnaB) complexed with ADP, at 3.3 resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: P.202, G.203, M.204, G.205, K.206, T.207, A.208, E.231, R.240, L.250, R.254, R.387, F.422, T.427 Chain B: R.411, Q.412 Ligands: MG.2 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.201, A:G.203, A:G.203, A:M.204, A:G.205, A:K.206, A:T.207, A:T.207, A:A.208, A:R.387, A:R.387, B:Q.412 Salt bridges: A:K.206, A:R.240 Water bridges: B:K.409 ADP.4: 15 residues within 4Å: Chain B: R.201, P.202, G.203, M.204, G.205, K.206, T.207, A.208, R.240, K.424, T.427 Chain E: Q.412, G.413, P.414 Ligands: MG.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.203, B:G.203, B:M.204, B:G.205, B:K.206, B:T.207, B:A.208 Salt bridges: B:K.206, B:R.240 ADP.6: 17 residues within 4Å: Chain C: P.202, G.203, M.204, G.205, K.206, T.207, A.208, E.231, R.240, L.250, R.254, R.387, F.422, T.427 Chain D: R.411, Q.412 Ligands: MG.7 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.201, C:G.203, C:G.203, C:M.204, C:G.205, C:K.206, C:T.207, C:A.208, C:R.387, C:R.387, D:Q.412 Salt bridges: C:K.206, C:R.240 Water bridges: D:K.409 ADP.9: 15 residues within 4Å: Chain A: Q.412, G.413, P.414 Chain D: R.201, P.202, G.203, M.204, G.205, K.206, T.207, A.208, R.240, K.424, T.427 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:G.203, D:G.203, D:M.204, D:G.205, D:K.206, D:T.207, D:A.208 Salt bridges: D:K.206, D:R.240 ADP.11: 17 residues within 4Å: Chain E: P.202, G.203, M.204, G.205, K.206, T.207, A.208, E.231, R.240, L.250, R.254, R.387, F.422, T.427 Chain F: R.411, Q.412 Ligands: MG.12 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:R.201, E:G.203, E:G.203, E:M.204, E:G.205, E:K.206, E:T.207, E:T.207, E:A.208, E:R.387, E:R.387, F:Q.412 Salt bridges: E:K.206, E:R.240 Water bridges: F:K.409 ADP.14: 15 residues within 4Å: Chain C: Q.412, G.413, P.414 Chain F: R.201, P.202, G.203, M.204, G.205, K.206, T.207, A.208, R.240, K.424, T.427 Ligands: MG.15 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:G.203, F:G.203, F:M.204, F:G.205, F:K.206, F:T.207, F:A.208 Salt bridges: F:K.206, F:R.240

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.207, E.231 Ligands: ADP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.207, A:E.231, A:E.231 MG.5: 3 residues within 4Å: Chain B: T.207, D.310 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.207 MG.7: 3 residues within 4Å: Chain C: T.207, E.231 Ligands: ADP.6 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.207, C:E.231, C:E.231 MG.10: 3 residues within 4Å: Chain D: T.207, D.310 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.207 MG.12: 3 residues within 4Å: Chain E: T.207, E.231 Ligands: ADP.11 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.207, E:E.231, E:E.231 MG.15: 3 residues within 4Å: Chain F: T.207, D.310 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.207

3 x SR: STRONTIUM ION(Non-functional Binders)

SR.3: 2 residues within 4Å: Chain A: H.118, E.122 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.118, A:E.122, A:E.122 SR.8: 2 residues within 4Å: Chain C: H.118, E.122 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.118, C:E.122, C:E.122 SR.13: 2 residues within 4Å: Chain E: H.118, E.122 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.118, E:E.122, E:E.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strycharska, M.S. et al., Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol.Cell (2013)

Release Date

2014-01-29

Peptides

Replicative DNA helicase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Replicative DNA helicase