SMTL ID : 5fy8.2 (1 other biounit)

Crystal structure of human JMJD2A in complex with D-threo-isocitrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: N81.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.2

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.256, H.262, C.328, S.329, C.330 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.256, A:H.262, A:C.328, A:C.330

1 x N81: 3-carboxy-2,3-dideoxy-D-erythro-pentaric acid(Non-covalent)

N81.3: 13 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, E.212, S.218, N.220, K.228, W.230, T.292, H.298, S.310 Ligands: NI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.207 Hydrogen bonds: A:S.218, A:N.220, A:S.310 Water bridges: A:K.263, A:K.263 Salt bridges: A:K.228, A:K.263, A:H.298

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: F.248, F.249, P.250, G.251, S.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.251, A:S.252

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 5 residues within 4Å: Chain A: C.256, E.257, A.258, F.259, L.260 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.256, A:F.259, A:L.260, A:Y.297, A:Y.297 EDO.6: 6 residues within 4Å: Chain A: R.317, Y.321, I.363, D.364, H.365, L.367 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.317, A:Y.321, A:H.365, A:L.367 EDO.7: 7 residues within 4Å: Chain A: D.213, M.214, R.261, L.327, C.328, M.334, V.335 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.213, A:D.213, A:M.214, A:C.328 Water bridges: A:C.328, A:V.335 EDO.8: 7 residues within 4Å: Chain A: I.89, P.90, A.91, P.92, A.156, D.157, V.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R. et al., Crystal Structure of Human Jmjd2A in Complex with D-Threo-Isocitrate. To be Published

Release Date

2016-03-16

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

LYSINE-SPECIFIC DEMETHYLASE 4A

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