SMTL ID : 7c9a.1

Human RAD51 post-synaptic complexes mutant (V273P, D274G)

Coordinates

PDB Format Compare

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: 46 residues within 4Å: Chain A: R.229, L.238, R.241, V.270, A.271, P.273, K.285, I.287, G.288, G.289, N.290 Chain B: R.229, L.238, S.239, R.241, Q.242, V.270, A.271, P.273, 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, P.273, I.287, G.288, G.289, N.290, I.291 Ligands: DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2, DA-DA-DA-DA-DA-DA-DA-DA-DA.2 Protein-ligand interaction information (PLIP) not available

1 x DA- DA- DA- DA- DA- DA- DA- DA- DA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')(Non-covalent)

DA-DA-DA-DA-DA-DA-DA-DA-DA.2: 18 residues within 4Å: Chain A: R.235, P.273 Chain B: R.235, G.236, P.273, G.274 Chain C: R.235, G.236, P.273 Ligands: DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1, DT-DT-DT-DT-DT-DT-DT-DT-DT.1 Protein-ligand interaction information (PLIP) not available

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

CA.3: 3 residues within 4Å: Chain A: T.134, E.163 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) CA.6: 1 residues within 4Å: Ligands: ANP.5 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain B: T.134, E.163 Ligands: ANP.8 No protein-ligand interaction detected (PLIP)

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

ANP.4: 21 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 Chain B: A.293, H.294, S.296, D.316, S.317, P.318, C.319, L.320, P.321 Ligands: CA.3 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: 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:E.163, B:C.319 ANP.5: 9 residues within 4Å: Chain A: A.293, H.294, D.316, S.317, P.318, C.319, L.320, P.321 Ligands: CA.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.316, A:C.319 ANP.8: 22 residues within 4Å: 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 Chain C: A.293, H.294, S.296, D.316, S.317, P.318, C.319, L.320, P.321 Ligands: CA.7 12 PLIP interactions: 1 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:C.319, 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:E.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, S.C. et al., Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures. Nat Commun (2021)

Release Date

2020-11-18

Peptides

DNA repair protein RAD51 homolog 1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA repair protein RAD51 homolog 1