SMTL ID : 7p0w.1

Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing thymine opposite to lesion)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

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

DT-DT-DT-PED-DT-DT-DT-DC-DT.1: 27 residues within 4Å: Chain A: S.54, Y.55, Q.56, R.96, L.97, Q.100, R.104, R.107, L.138, V.140, S.144, K.145, T.146, V.147, D.177, S.178, R.179, K.182 Ligands: DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, MPD.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.145 Hydrogen bonds: A:S.178, A:S.178, A:S.178, A:R.179 Water bridges: A:Q.56, A:R.179, A:K.182, A:K.182

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

DA-DG-DA-DA-DA-DT-DA-DA-DA.2: 17 residues within 4Å: Chain A: T.58, R.95, R.96, L.97, I.98, P.99, Q.100 Ligands: DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, NA.5, MPD.6 Protein-ligand interaction information (PLIP) not available

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

MPD.3: 9 residues within 4Å: Chain A: R.18, E.22, F.28, R.32, R.159, I.160, S.163, T.164, F.165 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.28, A:R.159 Hydrogen bonds: A:R.18, A:R.18 MPD.6: 9 residues within 4Å: Chain A: Q.56, R.96, L.97 Ligands: DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DT-DT-DT-PED-DT-DT-DT-DC-DT.1, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96

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

NA.4: 4 residues within 4Å: Chain A: G.132, A.135, R.136, K.142 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.132, A:R.136 Water bridges: A:R.136, A:R.136, A:R.136 NA.5: 5 residues within 4Å: Chain A: L.97, P.99, Q.100 Ligands: DA-DG-DA-DA-DA-DT-DA-DA-DA.2, DA-DG-DA-DA-DA-DT-DA-DA-DA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.97, A:Q.100

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

2022-07-13

Peptides

N-glycosylase/DNA lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-glycosylase/DNA lyase

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