SMTL ID : 5ivb.1

A High Resolution Structure of a Linked KDM5A Jmj Domain with Alpha-Ketoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

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

AKG.1: 12 residues within 4Å: Chain A: Y.151, Y.214, F.222, H.225, E.227, S.233, N.235, K.243, W.245, H.313, A.325 Ligands: MN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.214, A:F.222 Hydrogen bonds: A:Y.151, A:S.233, A:N.235 Water bridges: A:N.327 Salt bridges: A:K.243, A:H.313

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

MN.2: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: AKG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.225, A:E.227, A:H.313, H2O.2

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.75, Q.77, R.78, E.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.77 Water bridges: A:R.78, A:E.81 GOL.4: 5 residues within 4Å: Chain A: E.227, D.228, H.229, W.230, L.274 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227, A:D.228, A:H.229 GOL.5: 2 residues within 4Å: Chain A: N.298, C.300 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.298 Water bridges: A:R.54, A:R.54, A:T.129, A:T.129, A:T.129, A:N.298, A:N.298 GOL.6: 4 residues within 4Å: Chain A: F.115, E.145, D.146, V.147 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.145, A:E.145, A:D.146 Water bridges: A:I.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol (2016)

Release Date

2016-07-27

Peptides

Lysine-specific demethylase 5A,Lysine-specific demethylase 5A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5A,Lysine-specific demethylase 5A

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