SMTL ID : 7jl8.1 (1 other biounit)

Human PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 20 residues within 4Å: Chain A: G.74, R.76, Y.100, D.114, E.116, S.160, K.165, S.167, H.169, D.280, V.283, R.288, N.289, F.290, R.291, K.297 Chain B: T.3, G.4 Chain C: C.13 Ligands: CA.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.100 Hydrogen bonds: A:R.76, A:R.76, A:S.160, A:S.160, A:S.167, A:R.288, A:R.291 Water bridges: A:R.76 Salt bridges: A:K.165, A:K.165, A:H.169, A:R.291, A:R.291, A:K.297, A:K.297, A:K.297 pi-Cation interactions: A:R.76

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.114, E.116, K.165, H.169 Ligands: DTP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, A:D.114, A:E.116, H2O.1

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: L.133, D.262, F.265 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.262, A:D.262 GOL.6: 6 residues within 4Å: Chain A: Y.293, K.294, V.306, N.310, E.323, Y.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.293, A:K.294

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

EDO.4: 6 residues within 4Å: Chain A: W.87, K.91, D.319, V.320, S.321, Y.324 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.87, A:S.321 Water bridges: A:S.321, A:Y.324

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 8 residues within 4Å: Chain A: N.106, D.181, I.183, H.184, N.187, R.286, E.347, P.348 No protein-ligand interaction detected (PLIP) PEG.7: 9 residues within 4Å: Chain A: K.110, F.312, P.314, I.315, Q.325, L.328, S.329, N.334, R.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.315, A:N.334, A:N.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rechkoblit, O. et al., Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase. Nat Commun (2021)

Release Date

2021-06-30

Peptides

DNA-directed primase/polymerase protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-directed primase/polymerase protein

Related Entries With Identical Sequence