SMTL ID : 4lxl.1

Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- M3L- SER- THR- GLY- GLY- LYS: H3 peptide(Non-covalent)

ALA-ARG-M3L-SER-THR-GLY-GLY-LYS.1: 25 residues within 4Å: Chain A: I.92, Q.94, Q.105, Y.106, N.107, A.155, D.156, I.189, E.190, G.191, V.192, Y.196, Y.198, E.211, D.212, H.261, K.262, M.263, S.309, T.310, N.311, D.332, M.333, V.334 Ligands: PD2.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.92, A:Y.106, A:E.190, A:V.192 Hydrogen bonds: A:N.107, A:N.107, A:D.156, A:D.156, A:D.156, A:E.190, A:Y.196, A:H.261 Water bridges: A:E.190, A:E.190, A:H.261, A:K.262 Salt bridges: A:E.211

1 x PD2: PYRIDINE-2,4-DICARBOXYLIC ACID(Non-covalent)

PD2.2: 12 residues within 4Å: Chain A: Y.153, Y.198, F.206, H.209, E.211, N.219, K.227, W.229, K.262, H.297 Ligands: ALA-ARG-M3L-SER-THR-GLY-GLY-LYS.1, NI.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.206, A:W.229 Hydrogen bonds: A:Y.153, A:Y.198 Water bridges: A:K.262, A:K.262 Salt bridges: A:H.209, A:K.227, A:K.262 pi-Stacking: A:F.206

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

NI.3: 4 residues within 4Å: Chain A: H.209, E.211, H.297 Ligands: PD2.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.209, A:E.211, A:H.297, H2O.10

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: C.255, H.261, C.327, T.328, C.329 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.255, A:H.261, A:C.327, A:C.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W.-C. et al., Crystal structure of JMJD2B complexed with pyridine-2,4-dicarboxylic acid and H3K9me3. To be Published

Release Date

2014-07-30

Peptides

Lysine-specific demethylase 4B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 4B