SMTL ID : 7p8l.1

Crystal structure of Pyrococcus abyssi 8-oxoguanine DNA glycosylase (PabAGOG) in complex with dsDNA containing cytosine opposite to 8-oxoG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

1 x DT- DT- DT- 8OG- DT- DT- DT- DC- DT: DNA (5'-D(*TP*TP*TP*(8OG)P*TP*TP*TP*CP*T)-3')(Non-covalent)

DT-DT-DT-8OG-DT-DT-DT-DC-DT.1: 34 residues within 4Å: Chain A: Q.27, S.54, Y.55, Q.56, L.57, T.58, G.59, K.60, G.61, R.96, R.104, R.107, V.140, S.144, Q.145, T.146, F.149, K.152, P.175, D.177, S.178, R.179, I.180, D.211, W.215 Ligands: DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2, DA-DG-DA-DA-DA-DC-DA-DA-DA.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.27, A:Q.27, A:G.61, A:Q.145, A:K.152, A:P.175 Water bridges: A:S.178, A:R.179 Salt bridges: A:D.177, A:R.179, A:D.211 pi-Stacking: A:W.215, A:W.215 pi-Cation interactions: A:W.215

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

DA-DG-DA-DA-DA-DC-DA-DA-DA.2: 11 residues within 4Å: Chain A: R.95, R.96, L.97, Q.100 Ligands: DT-DT-DT-8OG-DT-DT-DT-DC-DT.1, DT-DT-DT-8OG-DT-DT-DT-DC-DT.1, DT-DT-DT-8OG-DT-DT-DT-DC-DT.1, DT-DT-DT-8OG-DT-DT-DT-DC-DT.1, DT-DT-DT-8OG-DT-DT-DT-DC-DT.1, DT-DT-DT-8OG-DT-DT-DT-DC-DT.1, DT-DT-DT-8OG-DT-DT-DT-DC-DT.1 Protein-ligand interaction information (PLIP) not available

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 4 residues within 4Å: Chain A: R.18, E.22, R.159, S.163 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.159 Hydrogen bonds: A:R.18, A:R.18 MPD.4: 4 residues within 4Å: Chain A: R.119, E.122, Y.123, S.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.129, A:S.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Franck, C. et al., Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing. Nucleic Acids Res. (2022)

Release Date

2022-08-03

Peptides

N-glycosylase/DNA lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-glycosylase/DNA lyase