SMTL ID : 3u4s.1 (1 other biounit)

Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- M3L- SER- CYS- GLY- GLY- LYS: HISTONE 3 TAIL ANALOG (T11C Peptide)(Non-covalent)

ALA-ARG-M3L-SER-CYS-GLY-GLY-LYS.1: 25 residues within 4Å: Chain A: I.93, Y.107, N.108, D.157, I.190, E.191, G.192, V.193, Y.197, Y.199, E.212, D.213, S.218, H.262, K.263, M.264, S.310, T.311, N.312, R.331, D.333, M.334, V.335 Ligands: NI.2, 08P.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.193, A:Y.197 Hydrogen bonds: A:N.108, A:N.108, A:N.108, A:D.157, A:D.157, A:E.191, A:Y.197, A:R.331, A:R.331, A:D.333 Water bridges: A:N.108, A:E.191, A:K.263 Salt bridges: A:E.212

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

NI.2: 5 residues within 4Å: Chain A: H.210, E.212, H.298 Ligands: ALA-ARG-M3L-SER-CYS-GLY-GLY-LYS.1, 08P.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.5

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 08P: N-(carboxycarbonyl)-D-cysteine(Non-covalent)

08P.4: 15 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-CYS-GLY-GLY-LYS.1, ALA-ARG-M3L-SER-CYS-GLY-GLY-LYS.1, NI.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.154, A:S.218, A:N.220, A:N.220, A:N.220, A:S.310 Salt bridges: A:K.228, A:H.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woon, E.C. et al., Linking of 2-Oxoglutarate and Substrate Binding Sites Enables Potent and Highly Selective Inhibition of JmjC Histone Demethylases. Angew.Chem.Int.Ed.Engl. (2012)

Release Date

2012-02-08

Peptides

Lysine-specific demethylase 4A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4A

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