SMTL ID : 5e6h.1

A Linked Jumonji Domain of the KDM5A Lysine Demethylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.225, E.227, H.313 Ligands: AKG.2 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

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

AKG.2: 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.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.214, A:F.222 Hydrogen bonds: A:Y.151, A:S.233, A:N.235 Salt bridges: A:K.243, A:H.313

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.82, E.83, S.141, I.281, M.282, N.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.83, A:I.281, A:N.283 GOL.4: 1 residues within 4Å: Chain A: A.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J.Biol.Chem. (2016)

Release Date

2015-12-16

Peptides

Lysine-specific demethylase 5A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5A

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