SMTL ID : 8gyk.1

CryoEM structure of the RAD51_ADP filament

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.14 Å

Oligo State

homo-octamer

Ligands

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

ADP.1: 11 residues within 4Å: Chain A: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, E.308, A.331 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.130, A:R.130, A:T.131, A:G.132, A:K.133, A:T.134, A:Q.135, A:R.170, A:R.170, A:E.308 Salt bridges: A:K.133, A:K.133 ADP.3: 15 residues within 4Å: Chain B: F.129, R.130, G.132, K.133, T.134, Q.135, E.163, T.165, R.170, E.308, R.310, I.329, N.330, A.331 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.130, B:G.132, B:T.134, B:T.134, B:Q.135, B:E.163, B:R.170, B:R.310 Salt bridges: B:R.130, B:R.130, B:K.133 ADP.5: 13 residues within 4Å: Chain C: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, R.310, I.329, N.330, A.331 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:R.130, C:R.130, C:T.131, C:G.132, C:K.133, C:T.134, C:T.134, C:Q.135, C:R.170, C:R.170, C:R.310 Salt bridges: C:K.133 ADP.7: 14 residues within 4Å: Chain D: F.129, R.130, G.132, K.133, T.134, Q.135, E.163, R.170, E.308, R.310, I.329, N.330, A.331 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:R.130, D:R.130, D:G.132, D:K.133, D:T.134, D:T.134, D:Q.135, D:Q.135, D:E.163, D:R.170, D:R.170, D:R.310 Salt bridges: D:K.133 ADP.9: 9 residues within 4Å: Chain E: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, A.331 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:R.130, E:R.130, E:R.130, E:T.131, E:G.132, E:K.133, E:T.134, E:T.134, E:Q.135, E:Q.135, E:R.170, E:R.310, E:R.310 Salt bridges: E:K.133 ADP.11: 11 residues within 4Å: Chain F: F.129, R.130, G.132, K.133, T.134, Q.135, E.308, R.310, I.329, A.331 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:R.130, F:R.130, F:G.132, F:T.134, F:T.134, F:Q.135, F:R.310 Salt bridges: F:K.133 ADP.13: 12 residues within 4Å: Chain G: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, I.329, N.330, A.331 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain G Hydrogen bonds: G:R.130, G:R.130, G:T.131, G:G.132, G:K.133, G:T.134, G:T.134, G:Q.135, G:Q.135, G:A.331 Salt bridges: G:K.133 ADP.15: 13 residues within 4Å: Chain H: F.129, R.130, G.132, K.133, T.134, Q.135, E.163, R.170, E.308, R.310, I.329, A.331 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:R.130, H:R.130, H:R.130, H:G.132, H:K.133, H:T.134, H:T.134, H:T.134, H:Q.135, H:E.163, H:R.170, H:R.170, H:R.310 Salt bridges: H:K.133

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.132, K.133, T.134 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.134 MG.4: 5 residues within 4Å: Chain B: R.130, T.131, G.132, K.133 Ligands: ADP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: K.133, T.134 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.134 MG.8: 5 residues within 4Å: Chain D: R.130, T.131, G.132, K.133 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain E: G.132, K.133, T.134, Q.135 Ligands: ADP.9 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain F: R.130, T.131, G.132, K.133 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain G: K.133, T.134, Q.135 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.134 MG.16: 5 residues within 4Å: Chain H: R.130, T.131, G.132, K.133 Ligands: ADP.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, S.C. et al., A RAD51-ADP double filament structure unveils the mechanism of filament dynamics in homologous recombination. Nat Commun (2023)

Release Date

2023-08-30

Peptides

DNA repair protein RAD51 homolog 1: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

DNA repair protein RAD51 homolog 1

Related Entries With Identical Sequence