SMTL ID : 5nwl.2 (1 other biounit)

Crystal structure of a human RAD51-ATP filament.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.93 Å

Oligo State

homo-heptamer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.134, T.165 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.134 MG.3: 4 residues within 4Å: Chain B: T.134, T.165, D.222 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.134, B:D.222 MG.5: 4 residues within 4Å: Chain C: T.134, T.165, D.222 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.134 MG.7: 4 residues within 4Å: Chain D: T.134, T.165, D.222 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.134 MG.9: 4 residues within 4Å: Chain E: T.134, T.165, D.222 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.134 MG.11: 4 residues within 4Å: Chain F: T.134, T.165, D.222 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.134 MG.13: 4 residues within 4Å: Chain G: T.134, T.165, D.222 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.134

7 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 14 residues within 4Å: Chain A: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.1 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.130, A:R.130, A:T.131, A:T.131, A:G.132, A:K.133, A:T.134, A:T.134, A:Q.135, A:R.170, A:R.170, A:Q.268, A:R.310 Salt bridges: A:K.133, A:K.133 ATP.4: 19 residues within 4Å: Chain A: S.317, P.318, C.319, L.320, P.321, E.322 Chain B: F.129, R.130, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.3 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.130, B:R.130, B:G.132, B:K.133, B:T.134, B:T.134, B:Q.135, B:Q.135, B:R.170, B:Q.268, B:R.310, A:C.319, A:E.322 Salt bridges: B:K.133, B:K.133 pi-Cation interactions: B:R.170 ATP.6: 21 residues within 4Å: Chain B: Y.315, D.316, S.317, C.319, L.320, P.321, E.322 Chain C: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.5 14 PLIP interactions: 11 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.130, C:R.130, C:T.131, C:G.132, C:K.133, C:T.134, C:Q.135, C:Q.268, C:R.310, B:C.319, B:E.322, B:E.322 Salt bridges: C:K.133, C:K.133 ATP.8: 22 residues within 4Å: Chain C: H.294, Y.315, D.316, S.317, C.319, L.320, P.321, E.322 Chain D: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.7 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:C.319, C:E.322, C:E.322, D:R.130, D:R.130, D:G.132, D:K.133, D:T.134, D:Q.135, D:R.170, D:Q.268, D:R.310 Salt bridges: D:K.133, D:K.133 ATP.10: 20 residues within 4Å: Chain D: S.317, P.318, C.319, L.320, P.321, E.322 Chain E: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.9 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:R.130, E:R.130, E:T.131, E:G.132, E:K.133, E:T.134, E:Q.135, E:Q.268, E:R.310, D:C.319, D:E.322, D:E.322, D:E.322 Salt bridges: E:K.133, E:K.133 ATP.12: 21 residues within 4Å: Chain E: Y.315, D.316, S.317, C.319, L.320, P.321, E.322 Chain F: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.11 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.130, F:R.130, F:T.131, F:G.132, F:K.133, F:T.134, F:Q.135, F:R.170, F:Q.268, F:R.310, E:C.319, E:E.322, E:E.322 Salt bridges: F:K.133, F:K.133 ATP.14: 20 residues within 4Å: Chain F: D.316, S.317, C.319, L.320, P.321, E.322 Chain G: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, R.170, Q.268, R.310, I.329, N.330, A.331 Ligands: MG.13 16 PLIP interactions: 14 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:R.130, G:R.130, G:R.130, G:G.132, G:K.133, G:T.134, G:T.134, G:Q.135, G:Q.135, G:R.170, G:Q.268, G:R.310, F:C.319, F:E.322 Salt bridges: G:K.133, G:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brouwer, I. et al., Two distinct conformational states define the interaction of human RAD51-ATP with single-stranded DNA. EMBO J. (2018)

Release Date

2018-03-07

Peptides

DNA repair protein RAD51 homolog 1: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
J

D
K

E
L

F
M

G
N

DNA repair protein RAD51 homolog 1

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