SMTL ID : 7ejc.1

human RAD51 presynaptic complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

1 x DT- DT- DT- DT- DT- DT- DT- DT- DT: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')(Non-covalent)

DT-DT-DT-DT-DT-DT-DT-DT-DT.1: 43 residues within 4Å: Chain A: R.229, L.238, R.241, Q.242, V.270, A.271, Q.272, V.273, K.285, I.287, G.288, N.290, I.291 Chain B: R.229, L.238, S.239, R.241, Q.242, V.270, A.271, Q.272, V.273, K.285, I.287, G.288, G.289, N.290, I.291 Chain C: R.229, L.238, S.239, R.241, Q.242, V.270, A.271, Q.272, V.273, K.285, I.287, G.288, G.289, N.290, I.291 Protein-ligand interaction information (PLIP) not available

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.134, E.163, T.165, D.222 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.134 MG.5: 5 residues within 4Å: Chain B: T.134, E.163, T.165, D.222 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.134 MG.9: 5 residues within 4Å: Chain C: T.134, E.163, T.165, D.222 Ligands: ANP.6 No protein-ligand interaction detected (PLIP)

3 x J46: 4-bromanyl-N-(4-bromophenyl)-3-[(phenylmethyl)sulfamoyl]benzamide(Non-covalent)

J46.3: 8 residues within 4Å: Chain A: P.56, K.58, E.59, Y.205, R.247, R.250, M.251, R.254 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.56, A:E.59, A:Y.205, A:R.250 Hydrogen bonds: A:E.59 J46.7: 10 residues within 4Å: Chain B: P.56, K.58, E.59, Y.205, R.247, R.250, M.251, R.254 Chain C: T.230, D.231 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.56, B:E.59, B:Y.205, B:R.247, B:R.250, B:M.251, B:R.254 Hydrogen bonds: B:E.59 J46.10: 11 residues within 4Å: Chain A: T.230, D.231 Chain C: P.56, K.58, E.59, Y.205, R.247, R.250, M.251, R.254, L.255 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:P.56, C:E.59, C:Y.205, C:R.250, C:M.251, C:R.254 Hydrogen bonds: C:E.59

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Covalent)

ANP.4: 12 residues within 4Å: Chain B: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, I.329, N.330 Ligands: MG.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.130, B:R.130, B:T.131, B:G.132, B:K.133, B:K.133, B:K.133, B:T.134, B:T.134, B:Q.135, B:Q.135, B:R.310 ANP.6: 20 residues within 4Å: Chain B: H.294, D.316, 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, I.329, N.330 Ligands: MG.9 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:K.133, C:K.133, C:T.134, C:Q.135, C:Q.135, C:R.310, B:H.294, B:P.318, B:E.322 ANP.8: 20 residues within 4Å: Chain A: F.129, R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, I.329, N.330 Chain C: H.294, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.2 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:R.130, A:R.130, A:T.131, A:G.132, A:K.133, A:K.133, A:K.133, A:T.134, A:T.134, A:Q.135, A:Q.135, A:R.310, C:H.294, C:P.318, C:E.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Mechanisms of distinctive mismatch tolerance between Rad51 and Dmc1 in homologous recombination. Nucleic Acids Res. (2021)

Release Date

2022-04-06

Peptides

DNA repair protein RAD51 homolog 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

DNA repair protein RAD51 homolog 1

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