SMTL ID : 7c98.1

Human DMC1 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: 47 residues within 4Å: Chain A: R.230, L.239, R.242, Q.243, T.271, A.272, D.273, P.274, G.289, G.290, H.291 Chain B: R.230, L.239, A.240, R.242, Q.243, T.271, A.272, D.273, P.274, G.289, G.290, H.291, I.292 Chain C: R.230, L.239, A.240, R.242, Q.243, Q.244, T.271, A.272, P.274, I.288, G.289, G.290, H.291, I.292 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: 17 residues within 4Å: Chain A: R.236, P.274, G.275 Chain B: R.236, G.237, G.275 Chain C: R.236, G.275 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)

CA.3: 3 residues within 4Å: Chain A: T.133, E.162 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain B: T.133, E.162, T.164 Ligands: ANP.6 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain C: T.133, E.162 Ligands: ANP.7 No protein-ligand interaction detected (PLIP)

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

ANP.4: 22 residues within 4Å: Chain A: F.128, R.129, T.130, G.131, K.132, T.133, Q.134, E.162, R.169, I.330, T.331 Chain B: A.294, H.295, S.297, D.317, S.318, P.319, E.320, M.321, P.322, E.323 Ligands: CA.3 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.131, A:K.132, A:K.132, A:K.132, A:T.133, A:T.133, A:Q.134, A:Q.134, A:R.169, B:H.295, B:D.317, B:D.317, B:S.318, B:S.318 ANP.6: 22 residues within 4Å: Chain B: F.128, R.129, T.130, G.131, K.132, T.133, Q.134, E.162, R.169, I.330, T.331, A.332, G.333 Chain C: A.294, H.295, S.297, D.317, S.318, P.319, E.320, M.321 Ligands: CA.5 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:T.130, B:G.131, B:K.132, B:K.132, B:K.132, B:T.133, B:T.133, B:Q.134, B:Q.134, B:R.169, B:G.333, C:H.295, C:D.317, C:E.320 ANP.7: 10 residues within 4Å: Chain C: F.128, R.129, G.131, K.132, T.133, Q.134, E.162, R.311, T.331 Ligands: CA.8 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.129, C:G.131, C:K.132, C:T.133, C:T.133, C:Q.134, C:Q.134, C:R.169, C:R.311

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

Meiotic recombination protein DMC1/LIM15 homolog: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Meiotic recombination protein DMC1/LIM15 homolog

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