SMTL ID : 8gd7.1

Loop Deleted DNA Polymerase Theta Polymerase Domain in Complex with Double Strand DNA Overhang and Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.24 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.401, Y.402, D.602 Ligands: DG3.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.401, A:D.602

1 x DG3: 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DG3.2: 13 residues within 4Å: Chain A: R.354, Q.404, E.406, F.430, R.450, K.454, Y.458, Y.462, D.602 Chain B: C.10, G.11 Chain C: C.14 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.406, A:Y.458 Hydrogen bonds: A:R.354, A:Q.404 Salt bridges: A:R.450, A:K.454, A:K.454, A:K.454 pi-Stacking: A:Y.458, A:Y.458

1 x Z5X: 2-(3-methyl-2-oxoimidazolidin-1-yl)-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)methylcarbamate(Non-covalent)

Z5X.3: 17 residues within 4Å: Chain A: L.407, V.422, V.429, S.432, I.433, E.436, W.437, I.456, C.457, I.460, I.461, M.473, Y.483, S.486, F.487, R.490, Y.491 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.433, A:I.433, A:E.436, A:I.456, A:I.460, A:Y.483, A:Y.483, A:F.487, A:F.487, A:Y.491 Hydrogen bonds: A:R.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fried, W. et al., Discovery of a small-molecule inhibitor that traps Pol theta on DNA and synergizes with PARP inhibitors. Nat Commun (2024)

Release Date

2024-06-19

Peptides

DNA polymerase theta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase theta