SMTL ID : 5h1c.1

Human RAD51 post-synaptic complexes

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: 45 residues within 4Å: Chain A: R.229, L.238, R.241, Q.242, A.271, Q.272, V.273, I.287, G.288, G.289, N.290, I.291 Chain B: R.229, L.238, S.239, R.241, Q.242, V.270, A.271, Q.272, V.273, I.287, G.288, G.289, N.290, I.291 Chain C: R.229, L.238, S.239, R.241, Q.242, A.271, I.287, G.288, G.289, 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: 19 residues within 4Å: Chain A: R.235, V.273, D.274 Chain B: R.235, G.236, D.274 Chain C: R.235, G.236, V.273, D.274 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 MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.134, D.222 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.222 MG.5: 3 residues within 4Å: Chain B: T.134, D.222 Ligands: ANP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.222 MG.8: 3 residues within 4Å: Chain C: T.134, D.222 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.222

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

ANP.4: 21 residues within 4Å: Chain A: R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, Q.268, R.310, I.329 Chain B: H.294, S.296, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.3 17 PLIP interactions: 14 interactions with chain A, 3 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:K.133, A:Q.135, A:Q.135, A:E.163, A:R.170, A:R.310, A:R.310, B:H.294, B:D.316, B:D.316 Salt bridges: A:K.133 ANP.6: 21 residues within 4Å: Chain B: R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, Q.268, R.310, I.329 Chain C: H.294, S.296, D.316, S.317, P.318, C.319, L.320, P.321, E.322 Ligands: MG.5 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.130, B:T.131, B:G.132, B:K.133, B:K.133, B:K.133, B:K.133, B:Q.135, B:Q.135, B:E.163, B:R.170, B:R.310, B:R.310, C:H.294, C:D.316, C:D.316 Salt bridges: B:K.133 ANP.7: 12 residues within 4Å: Chain C: R.130, T.131, G.132, K.133, T.134, Q.135, E.163, R.170, Q.268, R.310, I.329 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.130, C:T.131, C:G.132, C:K.133, C:K.133, C:K.133, C:K.133, C:Q.135, C:Q.135, C:E.163, C:E.163, C:R.170, C:R.310, C:R.310 Salt bridges: C:K.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, J. et al., Cryo-EM structures of human RAD51 recombinase filaments during catalysis of DNA-strand exchange. Nat. Struct. Mol. Biol. (2017)

Release Date

2016-12-21

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

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