SMTL ID : 5uqd.1

DPY-21 in complex with Fe(II) and alpha-Ketoglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

AKG.1: 12 residues within 4Å: Chain A: W.235, T.274, H.277, D.279, A.324, K.351, Y.410, L.412, H.418, F.420 Ligands: FE2.2, PG0.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.420, A:F.420 Hydrogen bonds: A:Y.410, A:Y.410 Water bridges: A:T.274, A:T.274 Salt bridges: A:K.351, A:H.418

1 x FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: H.277, D.279, H.418 Ligands: AKG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.277, A:D.279, A:H.418, H2O.1

2 x PG0: 2-(2-METHOXYETHOXY)ETHANOL(Non-functional Binders)

PG0.3: 8 residues within 4Å: Chain A: D.229, D.230, I.233, D.279, A.430, W.431, H.432 Ligands: AKG.1 No protein-ligand interaction detected (PLIP) PG0.4: 5 residues within 4Å: Chain A: H.94, R.97, Q.98, R.101, F.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brejc, K. et al., Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase. Cell (2017)

Release Date

2017-09-13

Peptides

DumPY: shorter than wild-type: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DumPY: shorter than wild-type