SMTL ID : 5fpv.1 (7 other biounits)

Crystal structure of human JMJD2A in complex with compound KDOAM20A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.189, E.191, H.277 Ligands: MMK.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.189, A:E.191, A:H.277, H2O.4

1 x MMK: 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid(Non-covalent)

MMK.2: 15 residues within 4Å: Chain A: Y.133, D.136, Y.176, Y.178, F.186, H.189, E.191, K.207, W.209, K.242, H.277, S.289, T.290, N.291 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.178, A:F.186, A:W.209 Hydrogen bonds: A:K.242 Salt bridges: A:K.207 pi-Stacking: A:F.186

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.235, H.241, C.307, S.308, C.309 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.235, A:H.241, A:C.307, A:C.309

3 x NI: NICKEL (II) ION(Non-covalent)

NI.4: 2 residues within 4Å: Chain A: G.230, S.231 No protein-ligand interaction detected (PLIP) NI.5: 2 residues within 4Å: Chain A: K.90, K.91 No protein-ligand interaction detected (PLIP) NI.6: 1 residues within 4Å: Chain A: Y.60 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. (2016)

Release Date

2016-01-13

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4A

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