SMTL ID : 5clc.1

Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog (9-mer B)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

DA-DA-DG-DC-DC-DZM-DC-DC-DC.1: 20 residues within 4Å: Chain A: Y.31, K.33, W.113, R.152, F.183, F.184, K.187, W.191, R.194, K.198, H.224 Ligands: DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2, DT-DG-DG-DG-DT-DG-DG-DC-DT.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.113 Hydrogen bonds: A:Y.31, A:R.152 Water bridges: A:Y.31, A:K.187, A:K.223 Salt bridges: A:K.187, A:R.194

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

DT-DG-DG-DG-DT-DG-DG-DC-DT.2: 15 residues within 4Å: Chain A: Q.42, T.43, P.44, R.47, T.122, K.160 Ligands: DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1, DA-DA-DG-DC-DC-DZM-DC-DC-DC.1 Protein-ligand interaction information (PLIP) not available

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mullins, E.A. et al., The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature (2015)

Release Date

2015-10-28

Peptides

AlkD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

AlkD

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