SMTL ID : 5fwj.2 (1 other biounit)

Crystal structure of human JARID1C in complex with KDM5-C49

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.406, C.409, C.429, H.432 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.406, A:C.409, A:C.429, A:H.432 ZN.2: 4 residues within 4Å: Chain A: C.420, C.423, C.437, C.439 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.420, A:C.423, A:C.437, A:C.439

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

MN.3: 4 residues within 4Å: Chain A: H.213, E.215, H.301 Ligands: MMK.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.213, A:E.215, A:H.301, H2O.6

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: R.333, R.336, H.432 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: P.323, R.326, K.367 No protein-ligand interaction detected (PLIP)

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

MMK.6: 16 residues within 4Å: Chain A: Y.139, D.142, G.195, W.200, Y.202, F.210, H.213, E.215, N.223, K.231, W.233, H.301, A.313, V.314, N.315 Ligands: MN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.202, A:W.233 Hydrogen bonds: A:Y.139 Water bridges: A:N.315 Salt bridges: A:K.231 pi-Stacking: A:F.210

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

2016-04-13

Peptides

HISTONE DEMETHYLASE JARID1C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

HISTONE DEMETHYLASE JARID1C

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