SMTL ID : 7olb.1

Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: Q.27, F.149, K.152, P.175, D.177, D.211, W.215 Ligands: CIT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.27, A:Q.27, A:K.152, A:D.211 EDO.2: 4 residues within 4Å: Chain A: P.167, Y.168, P.169, M.170 2 PLIP interactions: 2 interactions with chain A Water bridges: A:M.170, A:E.171 EDO.3: 2 residues within 4Å: Chain A: W.66, K.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.70 EDO.4: 12 residues within 4Å: Chain A: E.21, F.28, Y.124, M.127, G.155, Y.156, R.159, F.165, N.166, P.167, Y.168, H.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.124, A:G.155, A:N.166 EDO.5: 6 residues within 4Å: Chain A: E.67, Y.71, R.75, F.87, N.90, S.91 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.75, A:R.75, A:E.86 EDO.6: 4 residues within 4Å: Chain A: N.90, S.91, R.92, R.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.91, A:R.95 EDO.7: 4 residues within 4Å: Chain A: T.110, F.111, R.136, A.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.111 Water bridges: A:A.137

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.8: 16 residues within 4Å: Chain A: Q.27, S.54, Y.55, L.57, G.61, W.64, W.65, K.145, T.146, F.149, P.175, D.177, S.178, W.215 Ligands: EDO.1, NA.11 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.57, A:F.149 Hydrogen bonds: A:Q.27, A:S.54, A:S.54, A:W.65, A:K.145, A:T.146, A:D.177, A:W.215 Water bridges: A:S.178 Salt bridges: A:K.145, A:K.145

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

CL.9: 2 residues within 4Å: Chain A: R.136, K.142 Ligand excluded by PLIP

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

NA.10: 6 residues within 4Å: Chain A: S.35, I.38, D.39, S.40, F.43, V.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.35 NA.11: 7 residues within 4Å: Chain A: K.145, T.146, V.148, F.149, P.175, R.193 Ligands: CIT.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.146, A:F.149 Water bridges: A:V.148

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

2022-06-01

Peptides

N-glycosylase/DNA lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-glycosylase/DNA lyase

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