SMTL ID : 6h8p.2 (1 other biounit)

JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-mer

Ligands

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

NI.1: 6 residues within 4Å: Chain A: H.210, E.212, S.218, H.298 Chain B: K.9 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.210, A:E.212, A:H.298, H2O.3

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.256, F.259, 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 CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: F.249, P.250, G.251, S.252 Ligand excluded by PLIP

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

OGA.4: 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 Chain B: K.9 Ligands: NI.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.154, A:S.218, A:N.220 Water bridges: A:K.263 Salt bridges: A:K.228, A:H.298

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Y.81, R.120, F.224, F.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.120, A:R.120 Water bridges: A:Y.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walport, L.J. et al., Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26. FEBS Lett. (2018)

Release Date

2018-08-15

Peptides

Lysine-specific demethylase 4A: A
Histone H1.4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Lysine-specific demethylase 4A

Histone H1.4

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