SMTL ID : 4v2v.2 (1 other biounit)

JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (25-29) ARK(me3)SA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- M3L- SER- ALA: HISTONE H3.1T(Non-covalent)

ALA-ARG-M3L-SER-ALA.1: 18 residues within 4Å: Chain A: N.108, A.156, D.157, N.159, I.190, E.191, G.192, Y.197, Y.199, E.212, D.213, K.263, S.310, T.311, N.312, D.333, V.335 Ligands: OGA.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.156, A:E.191, A:Y.197 Hydrogen bonds: A:N.108, A:D.157, A:N.159, A:N.159, A:E.191, A:E.191, A:Y.197, A:D.333 Water bridges: A:K.263, A:K.263, A:K.263, A:K.263, A:R.331 Salt bridges: A:E.191, A:E.212

1 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 14 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: ALA-ARG-M3L-SER-ALA.1, NI.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.218, A:N.220, A:S.310 Water bridges: A:K.263 Salt bridges: A:K.228, A:H.298

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

NI.3: 4 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: OGA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.5

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.256, H.262, C.328, 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 CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, S.T. et al., Studies on the Catalytic Domains of Multiple Jmjc Oxygenases Using Peptide Substrates. Epigenetics (2014)

Release Date

2014-11-05

Peptides

LYSINE-SPECIFIC DEMETHYLASE 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 4A

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