SMTL ID : 8rxc.1

RadA helicase from Streptococcus pneumoniae coordinating dsDNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

5 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 19 residues within 4Å: Chain A: P.118, G.119, I.120, G.121, K.122, S.123, T.124, E.145, E.146, R.154, R.157, R.266, M.286 Chain B: N.273, R.274, G.276, S.277, T.278 Ligands: MG.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.119, A:I.120, A:G.121, A:K.122, A:S.123, A:T.124, A:E.145, A:E.145, A:R.266, B:N.273, B:T.278, B:T.278 Salt bridges: A:K.122, A:R.154 pi-Cation interactions: A:R.157 AGS.3: 21 residues within 4Å: Chain B: P.118, G.119, I.120, G.121, K.122, S.123, T.124, E.145, E.146, R.154, R.157, M.286, S.288 Chain C: K.272, N.273, R.274, F.275, G.276, S.277, T.278 Ligands: MG.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.119, B:G.119, B:G.121, B:K.122, B:S.123, B:T.124, B:E.145, B:E.146, B:S.288, C:R.274, C:T.278, C:T.278 Salt bridges: B:R.154 pi-Cation interactions: B:R.157 AGS.6: 18 residues within 4Å: Chain C: G.119, I.120, G.121, K.122, S.123, T.124, E.145, R.154, R.157, M.286 Chain D: H.249, K.272, N.273, R.274, F.275, G.276, S.277 Ligands: MG.5 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.119, C:G.121, C:K.122, C:S.123, C:T.124, C:T.124, C:R.157, C:R.157, D:H.249, D:K.272, D:K.272, D:S.277 Salt bridges: C:K.122, C:R.154 AGS.7: 20 residues within 4Å: Chain E: G.119, I.120, G.121, K.122, S.123, T.124, E.145, E.146, R.154, R.157, D.191, M.286, S.288 Chain F: N.273, R.274, F.275, G.276, S.277, T.278 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.119, E:G.119, E:I.120, E:G.121, E:K.122, E:S.123, E:T.124, E:T.124, E:E.145, E:S.288, F:G.276, F:T.278, F:T.278 Salt bridges: E:K.122, E:R.154, F:R.274 pi-Cation interactions: E:R.157 AGS.9: 19 residues within 4Å: Chain A: K.272, N.273, R.274, F.275, G.276, S.277, T.278 Chain F: P.118, G.119, G.121, K.122, S.123, T.124, E.145, E.146, R.157, D.191, M.286 Ligands: MG.10 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain F Hydrogen bonds: A:N.273, A:R.274, A:T.278, A:T.278, F:G.119, F:G.119, F:G.121, F:K.122, F:S.123, F:T.124, F:E.145, F:R.266 Salt bridges: F:K.122 pi-Cation interactions: F:R.157

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.123, E.146, D.191 Ligands: AGS.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.123, A:E.146 MG.4: 5 residues within 4Å: Chain B: S.123, E.145, E.146, D.191 Ligands: AGS.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.123, B:E.145 MG.5: 3 residues within 4Å: Chain C: S.123, E.145 Ligands: AGS.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.123, C:E.145 MG.8: 5 residues within 4Å: Chain E: S.123, E.145, E.146, D.191 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.123, E:D.191 MG.10: 5 residues within 4Å: Chain F: S.123, E.145, E.146, D.191 Ligands: AGS.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.123, F:D.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosa, L.T. et al., Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria. Embo J. (2024)

Release Date

2024-10-30

Peptides

DNA repair protein RadA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

E
F

F
E

DNA repair protein RadA