SMTL ID : 7ej6.1

Yeast Dmc1 presynaptic complex

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.223, L.232, S.233, R.235, Q.236, Q.237, Q.264, S.265, D.266, P.267, D.277, K.280, I.282, G.283, G.284, H.285, V.286 Chain B: R.223, L.232, S.233, R.235, Q.236, Q.237, Q.264, S.265, P.267, K.280, I.282, G.283, G.284, H.285, V.286 Chain C: R.223, L.232, R.235, Q.236, Q.264, S.265, D.266, P.267, D.277, K.280, I.282, G.283, G.284, H.285, V.286 Protein-ligand interaction information (PLIP) not available

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.128, E.157 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.157 MG.6: 3 residues within 4Å: Chain B: T.128, E.157 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.157 MG.7: 3 residues within 4Å: Chain C: T.128, E.157 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.128, C:E.157

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)(Non-covalent)

ATP.3: 25 residues within 4Å: Chain A: A.288, H.289, S.291, L.309, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Chain C: F.123, R.124, C.125, G.126, K.127, T.128, Q.129, R.164, Q.167, R.305, I.324, G.325 Ligands: MG.7 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.124, C:C.125, C:K.127, C:T.128, C:Q.129, C:Q.129, C:R.164, C:Q.167, C:Q.167, C:R.305, A:Q.310, A:S.312, A:S.312 Salt bridges: C:K.127, C:K.127, A:H.289 ATP.4: 24 residues within 4Å: Chain A: F.123, R.124, C.125, G.126, K.127, T.128, Q.129, R.164, Q.167, R.305, I.324, G.325 Chain B: A.288, H.289, L.309, Q.310, D.311, S.312, P.313, D.314, M.315, P.316, E.317 Ligands: MG.2 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.124, A:C.125, A:G.126, A:K.127, A:T.128, A:Q.129, A:Q.129, A:R.164, A:Q.167, A:Q.167, A:R.305, B:Q.310, B:S.312, B:S.312 Salt bridges: A:K.127, A:K.127, B:H.289 ATP.5: 13 residues within 4Å: Chain B: F.123, R.124, C.125, G.126, K.127, T.128, Q.129, R.164, Q.167, R.305, I.324, G.325 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.124, B:C.125, B:G.126, B:K.127, B:T.128, B:Q.129, B:Q.129, B:R.164, B:Q.167, B:Q.167, B:R.305 Salt bridges: B:K.127, B:K.127

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

2022-04-20

Peptides

HLJ1_G0016300.mRNA.1.CDS.1: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

HLJ1_G0016300.mRNA.1.CDS.1

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