SMTL ID : 8faz.1

Cryo-EM structure of the human BCDX2 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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

ADP.1: 12 residues within 4Å: Chain B: A.126, P.127, G.128, V.129, G.130, K.131, T.132, Q.133, E.161, R.168, R.322, I.341 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.126, B:G.128, B:G.128, B:V.129, B:G.130, B:K.131, B:T.132, B:T.132, B:Q.133, B:Q.133, B:R.168, B:R.322 Salt bridges: B:K.131, B:K.131

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 21 residues within 4Å: Chain B: H.307, Y.327, K.328, S.329, P.330, S.331, Q.332, K.333, E.334 Chain C: G.108, G.110, S.111, G.112, K.113, T.114, Q.115, N.138, R.145, Q.148, I.311 Ligands: MG.3 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:Y.327, B:K.328, B:S.329, B:S.331, B:E.334, B:E.334, C:G.110, C:S.111, C:G.112, C:K.113, C:K.113, C:K.113, C:T.114, C:Q.115, C:N.138, C:Q.148 ANP.4: 23 residues within 4Å: Chain C: F.270, K.297, S.298, S.299, R.300, Q.301, P.302, T.303 Chain D: P.49, E.50, G.51, T.52, G.53, K.54, T.55, E.56, H.86, R.91, F.253, I.272, G.273, E.274 Ligands: MG.5 20 PLIP interactions: 15 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:G.51, D:G.51, D:T.52, D:T.52, D:G.53, D:K.54, D:K.54, D:K.54, D:K.54, D:T.55, D:T.55, D:E.56, D:E.56, D:R.91, D:E.274, C:F.270, C:K.297, C:T.303, C:T.303, C:T.303

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain C: T.114, D.206 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.114 MG.5: 2 residues within 4Å: Chain D: T.55 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rawal, Y. et al., Structural insights into BCDX2 complex function in homologous recombination. Nature (2023)

Release Date

2023-06-21

Peptides

DNA repair protein RAD51 homolog 2: A
DNA repair protein RAD51 homolog 3: B
DNA repair protein RAD51 homolog 4: C
DNA repair protein XRCC2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
X

DNA repair protein RAD51 homolog 2

DNA repair protein RAD51 homolog 3

DNA repair protein RAD51 homolog 4

DNA repair protein XRCC2

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