SMTL ID : 6go7.1

TdT chimera (Loop1 of pol mu) - full DNA synapsis complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

monomer

Ligands

2 x DA- DA- DA- DA- DA- DC: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')(Non-covalent)

DA-DA-DA-DA-DA-DC.1: 24 residues within 4Å: Chain A: Q.42, Y.43, G.76, S.77, A.80, F.81, C.106, G.108, D.109, K.110, V.111, H.357, E.358 Ligands: DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.3, DT-DT-DT-DT-DT-DG-DC.6, DT-DT-DT-DT-DT-DG-DC.6, DT-DT-DT-DT-DT-DG-DC.6, DT-DT-DT-DT-DT-DG-DC.6, DT-DT-DT-DT-DT-DG-DC.6, DT-DT-DT-DT-DT-DG-DC.6 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DA-DA-DC.4: 20 residues within 4Å: Chain A: K.155, R.174, T.176, Q.177, Q.269, Y.270, H.271, R.272 Ligands: DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.5, DT-DT-DT-DT-DT-DG-DC.5, DT-DT-DT-DT-DT-DG-DC.5, DT-DT-DT-DT-DT-DG-DC.5, DT-DT-DT-DT-DT-DG-DC.5, DT-DT-DT-DT-DT-DG-DC.5 Protein-ligand interaction information (PLIP) not available

4 x DT- DT- DT- DT- DT- DG- DC: DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3')(Non-covalent)(Non-functional Binders)

DT-DT-DT-DT-DT-DG-DC.2: 23 residues within 4Å: Chain A: G.147, V.148, G.149, K.151, T.152, M.178, H.232, Q.269, H.271, R.294, F.296, R.323, W.341 Ligands: DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DT-DT-DT-DT-DT-DG-DC.5, DT-DT-DT-DT-DT-DG-DC.5, NA.7, DCT.8 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DG-DC.3: 17 residues within 4Å: Chain A: L.79, R.83, R.345, E.348, R.349, R.352, R.353, T.356, H.357 Ligands: DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DT-DT-DT-DT-DT-DG-DC.6, DCT.8 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DG-DC.5: 7 residues within 4Å: Ligands: DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.2, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4, DA-DA-DA-DA-DA-DC.4 Protein-ligand interaction information (PLIP) not available DT-DT-DT-DT-DT-DG-DC.6: 6 residues within 4Å: Ligands: DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DA-DA-DA-DA-DA-DC.1, DT-DT-DT-DT-DT-DG-DC.3 Protein-ligand interaction information (PLIP) not available

1 x NA: SODIUM ION(Non-functional Binders)

NA.7: 5 residues within 4Å: Chain A: T.143, V.145, F.146, V.148 Ligands: DT-DT-DT-DT-DT-DG-DC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.143

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.8: 16 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, G.231, H.232, D.233, D.235, G.340, W.341, G.343, R.345, E.348 Ligands: DT-DT-DT-DT-DT-DG-DC.2, DT-DT-DT-DT-DT-DG-DC.3, MG.9 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.223, A:H.232, A:D.233, A:R.345 Water bridges: A:R.226, A:R.226, A:K.228, A:K.228, A:R.294 Salt bridges: A:R.226, A:K.228, A:K.228, A:H.232, A:H.232

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: D.233, D.235 Ligands: DCT.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loc'h, J. et al., Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction. J.Biol.Chem. (2019)

Release Date

2019-06-05

Peptides

DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase

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