SMTL ID : 4nid.1

Crystal structure of AlkB protein with cofactors bound to dsDNA containing m6A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.120, D.122, H.176 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.120, A:D.122, A:H.176, H2O.1

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 14 residues within 4Å: Chain A: L.107, N.109, Y.111, L.117, H.120, D.122, S.134, H.176, I.178, R.193, N.195, T.197 Chain B: A.8 Ligands: MN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.117, A:I.178 Hydrogen bonds: A:N.109, A:N.109, A:Y.111, A:S.134, A:T.197 Water bridges: A:N.195, A:N.195 Salt bridges: A:H.120, A:R.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, C. et al., Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-04-16

Peptides

Alpha-ketoglutarate-dependent dioxygenase AlkB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alpha-ketoglutarate-dependent dioxygenase AlkB