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

Crystal structure of the human JMJD3 jumonji domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)(Non-functional Binders)

NI.1: 4 residues within 4Å: Chain A: H.217, E.219, H.297 Ligands: 8XQ.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.217, A:E.219, H2O.4, H2O.4 NI.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 1 residues within 4Å: Chain A: E.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.117, A:E.117

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: I.15, Y.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.16 EDO.5: 3 residues within 4Å: Chain A: Q.30, D.34, Q.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.30, A:Q.319 EDO.6: 3 residues within 4Å: Chain A: D.160, M.200, N.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.160, A:N.201, A:N.201 EDO.7: 7 residues within 4Å: Chain A: S.57, T.58, Q.111, G.231, P.232, C.305, N.306 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.58, A:T.58, A:N.306

1 x 8XQ: 8-hydroxyquinoline-5-carboxylic acid(Non-covalent)

8XQ.8: 13 residues within 4Å: Chain A: F.155, Y.206, K.208, T.214, H.217, E.219, N.227, W.237, I.291, H.297, V.299, N.307 Ligands: NI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.206, A:T.214, A:W.237, A:V.299 Hydrogen bonds: A:T.214, A:N.227 Water bridges: A:T.214, A:S.225 Salt bridges: A:K.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Che, K.H. et al., Crystal Structure of the Human Jmjd3 Jumonji Domain. To be Published

Release Date

2010-11-24

Peptides

LYSINE-SPECIFIC DEMETHYLASE 6B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 6B

Related Entries With Identical Sequence