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

Crystal structure of human JMJD2A in complex with fumarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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 FUM: FUMARIC ACID(Non-covalent)

FUM.2: 9 residues within 4Å: Chain A: Y.154, Y.199, F.207, H.210, N.220, K.228, W.230, H.298 Ligands: MN.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.207, A:F.207 Hydrogen bonds: A:N.220 Water bridges: A:S.310 Salt bridges: A:H.210, A:K.228, A:H.298

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.249, A:G.251, A:S.252

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

MN.4: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: FUM.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.2, H2O.2

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

EDO.5: 9 residues within 4Å: Chain A: Y.143, W.144, S.206, F.207, W.209, L.266, I.267, A.299, G.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.267, A:I.267, A:G.300 EDO.6: 6 residues within 4Å: Chain A: Y.128, N.150, P.152, M.202, W.203, K.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.150, A:W.203, A:K.204 EDO.7: 3 residues within 4Å: Chain A: G.102, S.268, L.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R. et al., Crystal Structure of Human Jmjd2A in Complex with Fumarate. To be Published

Release Date

2016-03-23

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

LYSINE-SPECIFIC DEMETHYLASE 4A

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