SMTL ID : 1pzn.2 (1 other biounit)

Rad51 (RadA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-heptamer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: E.139, F.140, G.141, S.142, G.143, K.144, T.145 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.141, A:S.142, A:G.143, A:K.144, A:T.145, A:T.145 Water bridges: A:G.143, A:K.144, A:Q.146 Salt bridges: A:K.144 SO4.7: 7 residues within 4Å: Chain B: E.139, F.140, G.141, S.142, G.143, K.144, T.145 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.141, B:S.142, B:G.143, B:K.144, B:T.145, B:T.145 Salt bridges: B:K.144 SO4.13: 6 residues within 4Å: Chain C: E.139, G.141, S.142, G.143, K.144, T.145 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.139, C:G.141, C:S.142, C:G.143, C:K.144, C:T.145, C:T.145 Salt bridges: C:K.144 SO4.17: 7 residues within 4Å: Chain D: E.139, F.140, G.141, S.142, G.143, K.144, T.145 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:E.139, D:G.141, D:S.142, D:G.143, D:K.144, D:T.145, D:T.145 Water bridges: D:K.144 Salt bridges: D:K.144 SO4.19: 7 residues within 4Å: Chain E: E.139, F.140, G.141, S.142, G.143, K.144, T.145 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:G.141, E:S.142, E:G.143, E:K.144, E:T.145, E:T.145 Salt bridges: E:K.144 SO4.22: 7 residues within 4Å: Chain F: E.139, F.140, G.141, S.142, G.143, K.144, T.145 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.141, F:S.142, F:G.143, F:K.144, F:T.145, F:T.145, F:T.145 Salt bridges: F:K.144 SO4.27: 8 residues within 4Å: Chain G: E.139, F.140, G.141, S.142, G.143, K.144, T.145 Ligands: MPD.29 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.141, G:G.141, G:S.142, G:G.143, G:K.144, G:T.145, G:T.145 Water bridges: G:Q.146 Salt bridges: G:K.144

9 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 3 residues within 4Å: Chain A: R.99 Chain B: Y.201, K.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.99 IMD.3: 3 residues within 4Å: Chain A: K.317, G.321, R.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.321, A:R.323 IMD.4: 2 residues within 4Å: Chain A: K.319, G.320 No protein-ligand interaction detected (PLIP) IMD.5: 3 residues within 4Å: Chain A: Y.201, E.224 Chain G: R.99 No protein-ligand interaction detected (PLIP) IMD.8: 6 residues within 4Å: Chain A: R.251 Chain B: G.250, R.251, G.252, A.253, L.254 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.251, B:A.253, B:L.254 IMD.9: 3 residues within 4Å: Chain B: K.319, G.320, G.321 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.321 IMD.10: 2 residues within 4Å: Chain B: G.321, R.323 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:R.323 IMD.14: 2 residues within 4Å: Chain B: R.99 Chain C: Y.201 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.99 pi-Stacking: C:Y.201 IMD.23: 5 residues within 4Å: Chain E: R.99 Chain F: Y.201, K.221, E.224, L.225 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.99, F:E.224

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: K.198 Chain G: R.99 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain A Hydrogen bonds: G:R.99, A:K.198, A:K.198 GOL.11: 2 residues within 4Å: Chain A: R.99 Chain B: K.198 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.198, B:K.198, A:R.99 GOL.15: 2 residues within 4Å: Chain C: R.99 Chain D: K.198 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:K.198, C:R.99 GOL.16: 2 residues within 4Å: Chain B: R.99 Chain C: K.198 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.198, C:K.198 GOL.18: 7 residues within 4Å: Chain D: T.96, M.98, Y.103, K.106, N.273 Chain E: A.203, R.204 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:N.273, E:R.204 GOL.20: 2 residues within 4Å: Chain D: R.99 Chain E: K.198 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:K.198, E:K.198, D:R.99, D:R.99 GOL.24: 6 residues within 4Å: Chain F: Q.156, L.157, L.191, E.195, H.199, R.230 No protein-ligand interaction detected (PLIP) GOL.25: 2 residues within 4Å: Chain E: R.99 Chain F: K.198 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.198, F:K.198 GOL.26: 2 residues within 4Å: Chain F: R.99 Chain G: K.198 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:K.198, G:K.198, F:R.99

4 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.12: 8 residues within 4Å: Chain A: T.58, A.61, K.263, A.266, D.267 Chain B: N.207, N.209, H.210 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.209, A:A.266 Hydrogen bonds: B:N.207 MPD.21: 5 residues within 4Å: Chain D: R.99, E.102 Chain E: Y.201, K.221, E.224 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.221, E:K.221, E:E.224 MPD.28: 2 residues within 4Å: Chain G: R.183, Q.187 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.183, G:Q.187 MPD.29: 3 residues within 4Å: Chain G: Q.146, I.342 Ligands: SO4.27 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Q.146, G:I.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, D.S. et al., Full-length archaeal Rad51 structure and mutants: Mechanisms for RAD51 assembly and control by BRCA2. Embo J. (2003)

Release Date

2003-09-09

Peptides

DNA repair and recombination protein rad51: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

DNA repair and recombination protein rad51

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