SMTL ID : 8pbd.1

RAD51 filament on dsDNA bound by the BRCA2 c-terminus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-9-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.2, CA.3 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:T.134, A:Q.135, A:Q.135, A:R.170 Salt bridges: A:K.133, A:K.133 ATP.5: 23 residues within 4Å: Chain A: A.293, H.294, S.317, P.318, C.319, L.320, P.321, E.322 Chain B: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.4, CA.6 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.130, B:R.130, B:T.131, B:G.132, B:K.133, B:T.134, B:T.134, B:Q.135, B:Q.135, A:C.319 Salt bridges: B:K.133, B:K.133, A:H.294 ATP.8: 23 residues within 4Å: Chain B: A.293, H.294, S.317, P.318, C.319, L.320, P.321, E.322 Chain C: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.7, CA.9 13 PLIP interactions: 11 interactions with chain C, 2 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:T.134, C:Q.135, C:Q.135, B:C.319 Salt bridges: C:K.133, C:K.133, B:H.294 ATP.11: 23 residues within 4Å: Chain C: A.293, H.294, S.317, P.318, C.319, L.320, P.321, E.322 Chain D: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.10, CA.12 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:C.319, D:R.130, D:R.130, D:T.131, D:G.132, D:K.133, D:T.134, D:T.134, D:Q.135, D:Q.135 Salt bridges: C:H.294, D:K.133, D:K.133 ATP.14: 24 residues within 4Å: Chain D: A.293, H.294, D.316, 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, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.13, CA.15 13 PLIP interactions: 11 interactions with chain E, 2 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:T.134, E:Q.135, E:Q.135, D:C.319 Salt bridges: E:K.133, E:K.133, D:H.294 ATP.17: 23 residues within 4Å: Chain E: A.293, H.294, S.317, P.318, C.319, L.320, P.321, E.322 Chain F: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.16, CA.18 13 PLIP interactions: 11 interactions with chain F, 2 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:T.134, F:Q.135, F:Q.135, E:C.319 Salt bridges: F:K.133, F:K.133, E:H.294 ATP.20: 24 residues within 4Å: Chain F: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain G: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.19, CA.21 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain G Hydrogen bonds: F:C.319, 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 Salt bridges: F:H.294, G:K.133, G:K.133 ATP.23: 24 residues within 4Å: Chain G: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain H: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.22, CA.24 13 PLIP interactions: 11 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:R.130, H:R.130, H:T.131, H:G.132, H:K.133, H:T.134, H:T.134, H:Q.135, H:Q.135, G:C.319 Salt bridges: H:K.133, H:K.133, G:H.294 ATP.26: 24 residues within 4Å: Chain H: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain I: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.25, CA.27 13 PLIP interactions: 11 interactions with chain I, 2 interactions with chain H Hydrogen bonds: I:R.130, I:R.130, I:T.131, I:G.132, I:K.133, I:T.134, I:T.134, I:Q.135, I:Q.135, H:C.319 Salt bridges: I:K.133, I:K.133, H:H.294 ATP.29: 24 residues within 4Å: Chain I: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Chain J: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, R.310, I.329, N.330, A.331 Ligands: CA.28, CA.30 13 PLIP interactions: 11 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:R.130, J:R.130, J:T.131, J:G.132, J:K.133, J:T.134, J:T.134, J:Q.135, J:Q.135, I:C.319 Salt bridges: J:K.133, J:K.133, I:H.294

20 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 4 residues within 4Å: Chain A: T.134, E.163, T.165 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.134, A:E.163 CA.3: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) CA.4: 5 residues within 4Å: Chain A: A.293, H.294, S.296, D.316 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:A.293, A:S.296 CA.6: 4 residues within 4Å: Chain B: T.134, E.163, T.165 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.134, B:E.163 CA.7: 5 residues within 4Å: Chain B: A.293, H.294, S.296, D.316 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:A.293, B:S.296 CA.9: 4 residues within 4Å: Chain C: T.134, E.163, T.165 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.134, C:E.163 CA.10: 5 residues within 4Å: Chain C: A.293, H.294, S.296, D.316 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:A.293, C:S.296 CA.12: 4 residues within 4Å: Chain D: T.134, E.163, T.165 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.134, D:E.163 CA.13: 5 residues within 4Å: Chain D: A.293, H.294, S.296, D.316 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:A.293, D:S.296 CA.15: 4 residues within 4Å: Chain E: T.134, E.163, T.165 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.134, E:E.163 CA.16: 5 residues within 4Å: Chain E: A.293, H.294, S.296, D.316 Ligands: ATP.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:A.293, E:S.296 CA.18: 4 residues within 4Å: Chain F: T.134, E.163, T.165 Ligands: ATP.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.134, F:E.163 CA.19: 5 residues within 4Å: Chain F: A.293, H.294, S.296, D.316 Ligands: ATP.20 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:A.293, F:S.296 CA.21: 4 residues within 4Å: Chain G: T.134, E.163, T.165 Ligands: ATP.20 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.134, G:E.163 CA.22: 5 residues within 4Å: Chain G: A.293, H.294, S.296, D.316 Ligands: ATP.23 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:A.293, G:S.296 CA.24: 4 residues within 4Å: Chain H: T.134, E.163, T.165 Ligands: ATP.23 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.134, H:E.163 CA.25: 5 residues within 4Å: Chain H: A.293, H.294, S.296, D.316 Ligands: ATP.26 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:A.293, H:S.296 CA.27: 4 residues within 4Å: Chain I: T.134, E.163, T.165 Ligands: ATP.26 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.134, I:E.163 CA.28: 5 residues within 4Å: Chain I: A.293, H.294, S.296, D.316 Ligands: ATP.29 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:A.293, I:S.296 CA.30: 4 residues within 4Å: Chain J: T.134, E.163, T.165 Ligands: ATP.29 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.134, J:E.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Appleby, R. et al., Structural basis for stabilisation of the RAD51 nucleoprotein filament by BRCA2. Nat Commun (2023)

Release Date

2023-11-15

Peptides

DNA repair protein RAD51 homolog 1: ABCDEFGHIJ
Breast cancer type 2 susceptibility protein: KLMNOPQRS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

DNA repair protein RAD51 homolog 1

Breast cancer type 2 susceptibility protein

Related Entries With Identical Sequence