SMTL ID : 8u0o.1

Synaptic complex of human DNA polymerase Lambda DL variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: S.110, I.112, A.115 Ligands: DG-DC-DC-DG-DC-DG-DT-DA.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.112, A:A.115

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 5 residues within 4Å: Chain A: R.157, S.188, C.196, G.197, D.198 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.188, A:S.188, A:G.197, A:D.198, A:D.198 Water bridges: A:S.188, A:D.198 Salt bridges: A:R.157

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: N.111, W.113 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 1 residues within 4Å: Chain A: R.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.190 Water bridges: A:E.322 EDO.5: 5 residues within 4Å: Chain A: F.265, L.269, P.320, T.321, E.322 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.322

1 x DA- DC- DG- DC- DG- DG- DC- DA: DNA (5'-D(*AP*CP*GP*CP*GP*GP*CP*A)-3')(Non-covalent)

DA-DC-DG-DC-DG-DG-DC-DA.6: 13 residues within 4Å: Chain A: T.142, Q.143, V.233, K.234, G.235 Ligands: DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7, DG-DC-DC-DG-DC-DG-DT-DA.7 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG- DC- DG- DT- DA: DNA (5'-D(P*GP*CP*CP*GP*CP*GP*TP*A)-3')(Non-covalent)

DG-DC-DC-DG-DC-DG-DT-DA.7: 22 residues within 4Å: Chain A: I.112, W.113, G.114, A.115, G.116, T.117, K.118, T.119, K.238, L.240, R.254, D.256, Y.271, F.272 Ligands: NA.1, DA-DC-DG-DC-DG-DG-DC-DA.6, DA-DC-DG-DC-DG-DG-DC-DA.6, DA-DC-DG-DC-DG-DG-DC-DA.6, DA-DC-DG-DC-DG-DG-DC-DA.6, DA-DC-DG-DC-DG-DG-DC-DA.6, DA-DC-DG-DC-DG-DG-DC-DA.6, DA-DC-DG-DC-DG-DG-DC-DA.6 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaminski, A.M. et al., DNA polymerase lambda Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining. DNA Repair (Amst) (2024)

Release Date

2024-03-13

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda