SMTL ID : 5lkm.1

RadA bound to dTDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-hexamer

Ligands

6 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 13 residues within 4Å: Chain A: P.97, G.98, I.99, G.100, K.101, S.102, T.103, R.133, R.136, H.213, S.267, G.268 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.103 Hydrogen bonds: A:G.98, A:I.99, A:G.100, A:K.101, A:S.102, A:S.102, A:T.103, A:T.103, A:R.136 Salt bridges: A:K.101, A:R.133, A:H.213 TYD.3: 15 residues within 4Å: Chain B: P.97, G.98, I.99, G.100, K.101, S.102, T.103, E.125, R.133, R.136, H.213, S.267, G.268 Chain C: T.257 Ligands: MG.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:T.103 Hydrogen bonds: B:G.98, B:I.99, B:G.100, B:K.101, B:S.102, B:S.102, B:T.103, B:T.103, B:R.136, C:T.257 Salt bridges: B:K.101, B:R.133, B:H.213 TYD.5: 14 residues within 4Å: Chain C: P.97, G.98, I.99, G.100, K.101, S.102, T.103, R.133, R.136, L.137, H.213, S.267, G.268 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:T.103, C:L.137 Hydrogen bonds: C:G.98, C:I.99, C:G.100, C:K.101, C:S.102, C:S.102, C:T.103, C:T.103, C:R.136, C:S.267 Salt bridges: C:K.101, C:R.133, C:H.213 TYD.7: 13 residues within 4Å: Chain D: P.97, G.98, I.99, G.100, K.101, S.102, T.103, R.133, R.136, H.213, S.267, G.268 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:T.103 Hydrogen bonds: D:G.98, D:I.99, D:G.100, D:K.101, D:S.102, D:S.102, D:T.103, D:T.103, D:R.136 Salt bridges: D:K.101, D:R.133, D:H.213 TYD.9: 15 residues within 4Å: Chain E: P.97, G.98, I.99, G.100, K.101, S.102, T.103, E.125, R.133, R.136, H.213, S.267, G.268 Chain F: T.257 Ligands: MG.10 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:T.103 Hydrogen bonds: E:G.98, E:I.99, E:G.100, E:K.101, E:S.102, E:S.102, E:T.103, E:T.103, E:R.136, F:T.257 Salt bridges: E:K.101, E:R.133, E:H.213 TYD.11: 14 residues within 4Å: Chain F: P.97, G.98, I.99, G.100, K.101, S.102, T.103, R.133, R.136, L.137, H.213, S.267, G.268 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:T.103, F:L.137 Hydrogen bonds: F:G.98, F:I.99, F:G.100, F:K.101, F:S.102, F:S.102, F:T.103, F:T.103, F:R.136, F:S.267 Salt bridges: F:K.101, F:R.133, F:H.213

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.102, E.124 Ligands: TYD.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.102 MG.4: 4 residues within 4Å: Chain B: S.102, E.124, H.213 Ligands: TYD.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:S.102, B:E.124 MG.6: 4 residues within 4Å: Chain C: S.102, E.124, D.170 Ligands: TYD.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.102, C:E.124 MG.8: 3 residues within 4Å: Chain D: S.102, E.124 Ligands: TYD.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.102 MG.10: 4 residues within 4Å: Chain E: S.102, E.124, H.213 Ligands: TYD.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:S.102, E:E.124 MG.12: 4 residues within 4Å: Chain F: S.102, E.124, D.170 Ligands: TYD.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:S.102, F:E.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marie, L. et al., Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension. Nat Commun (2017)

Release Date

2017-06-07

Peptides

DNA repair protein RadA: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

DNA repair protein RadA