SMTL ID : 7lxj.1

Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

DA-DG-DC-DA-DA-ORP-DG-DG-DC.1: 27 residues within 4Å: Chain A: R.30, Y.31, K.33, W.112, W.113, D.117, R.152, F.183, F.184, K.187, W.191, R.194, E.195, K.198, K.223, H.224 Ligands: DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, CA.4, YNY.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.113 Hydrogen bonds: A:D.117, A:D.117, A:R.152 Salt bridges: A:R.194

1 x DT- DG- DC- DC- DT- DT- DT- DG- DC: DNA (5'-D(*TP*GP*CP*CP*TP*TP*TP*GP*C)-3')(Non-covalent)

DT-DG-DC-DC-DT-DT-DT-DG-DC.2: 14 residues within 4Å: Chain A: Q.42, T.43, P.44, R.47, K.160 Ligands: DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, YNY.5 Protein-ligand interaction information (PLIP) not available

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: D.146 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.146, H2O.3, H2O.3, H2O.4, H2O.5 CA.4: 2 residues within 4Å: Chain A: K.187 Ligands: DA-DG-DC-DA-DA-ORP-DG-DG-DC.1 No protein-ligand interaction detected (PLIP)

1 x YNY: methyl (8R)-8-{[(4P)-6-amino-3H-purin-3-yl]methyl}-4-hydroxy-6-(5,6,7-trimethoxy-1H-indole-2-carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carboxylate(Non-covalent)

YNY.5: 20 residues within 4Å: Chain A: M.28, Y.31, M.32, W.113, D.114, P.121, L.159, K.160, W.191, E.195 Ligands: DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DA-DG-DC-DA-DA-ORP-DG-DG-DC.1, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2, DT-DG-DC-DC-DT-DT-DT-DG-DC.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.31 Water bridges: A:D.114, A:D.114, A:S.118 pi-Stacking: A:W.113, A:W.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullins, E.A. et al., Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites. Nat Commun (2021)

Release Date

2021-11-17

Peptides

DNA-7-methylguanine glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-7-methylguanine glycosylase

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