SMTL ID : 7c9c.1

Human DMC1 pre-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: 43 residues within 4Å: Chain A: R.230, L.239, R.242, Q.243, T.271, A.272, P.274, P.284, K.286, I.288, 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, P.284, K.286, I.288, G.289, G.290, H.291, I.292 Chain C: R.230, L.239, A.240, R.242, Q.243, T.271, A.272, P.274, K.286, I.288, G.289, G.290, H.291, I.292 Protein-ligand interaction information (PLIP) not available

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: T.133, E.162 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.162 CA.4: 3 residues within 4Å: Chain B: T.133, E.162 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.162 CA.6: 3 residues within 4Å: Chain C: T.133, E.162 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.162

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

ANP.3: 25 residues within 4Å: Chain A: F.128, R.129, T.130, G.131, K.132, T.133, Q.134, E.162, R.169, R.311, I.330, T.331, A.332 Chain B: A.294, H.295, S.297, Y.316, D.317, S.318, P.319, E.320, M.321, P.322, E.323 Ligands: CA.2 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:F.128, A:R.129, A:T.130, A:G.131, A:K.132, A:K.132, A:T.133, A:T.133, A:Q.134, A:R.311, B:H.295, B:Y.316 ANP.5: 24 residues within 4Å: Chain B: F.128, R.129, T.130, G.131, K.132, T.133, Q.134, E.162, R.169, R.311, I.330, T.331, A.332 Chain C: A.294, H.295, Y.316, D.317, S.318, P.319, E.320, M.321, P.322, E.323 Ligands: CA.4 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:F.128, B:R.129, 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:R.311, C:H.295, C:Y.316 ANP.7: 14 residues within 4Å: Chain C: F.128, R.129, T.130, G.131, K.132, T.133, Q.134, E.162, R.169, R.311, I.330, T.331, A.332 Ligands: CA.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:F.128, C:T.130, C:G.131, C:K.132, C:K.132, C:T.133, C:T.133, C:Q.134, C:Q.134, 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

2020-11-25

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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