SMTL ID : 2oq6.1 (1 other biounit)

Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- M3L- SER- THR- GLY- GLY- ALY: synthetic peptide(Non-covalent)

ALA-ARG-M3L-SER-THR-GLY-GLY-ALY.1: 28 residues within 4Å: Chain A: I.93, Q.106, Y.107, N.108, I.109, Q.110, A.156, D.157, N.159, I.190, E.191, G.192, V.193, Y.197, Y.199, E.212, D.213, H.262, K.263, M.264, S.310, T.311, N.312, R.331, D.333, M.334, V.335 Ligands: OGA.4 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.93, A:I.109, A:A.156, A:V.193, A:Y.197, A:V.335 Hydrogen bonds: A:N.108, A:N.108, A:Q.110, A:D.157, A:D.157, A:N.159, A:E.191, A:Y.197, A:H.262, A:R.331, A:D.333 Water bridges: A:E.191, A:K.263 Salt bridges: A:E.191, A:E.212, A:R.331

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

NI.2: 4 residues within 4Å: Chain A: H.210, E.212, H.298 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.7

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 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 OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.4: 13 residues within 4Å: Chain A: Y.154, 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-THR-GLY-GLY-ALY.1, NI.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.218, A:N.220, A:S.310 Salt bridges: A:K.228, A:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ng, S.S. et al., Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity. Nature (2007)

Release Date

2007-03-13

Peptides

JmjC domain-containing histone demethylation protein 3A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

JmjC domain-containing histone demethylation protein 3A

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