SMTL ID : 5uuf.1

Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (12-mer product complex)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x YTA: yatakemycin-adenine nucleobase adduct(Non-covalent)

YTA.1: 23 residues within 4Å: Chain A: K.24, P.27, M.28, Y.31, M.32, Q.42, W.113, D.114, D.117, P.121, L.159, K.160, W.191 Chain B: C.4, A.5, X.6, A.7 Chain C: T.6, T.7, T.8, G.9, G.10, G.11 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.31, A:Y.31 Hydrogen bonds: A:Q.42, A:K.160 Water bridges: A:K.24, A:T.43, A:T.43, A:D.114, A:D.117, A:D.117, A:S.118 pi-Stacking: A:W.113, A:W.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullins, E.A. et al., Toxicity and repair of DNA adducts produced by the natural product yatakemycin. Nat. Chem. Biol. (2017)

Release Date

2017-07-19

Peptides

DNA-7-methylguanine glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA-7-methylguanine glycosylase

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