5FZ4: Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (3R)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol (N10057a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

PDB ID: 5FZ4Download
MMDB ID: 137751
PDB Deposition Date: 2016/3/10
Updated in MMDB: 2016/03
Experimental Method:
x-ray diffraction
Resolution: 2.07  Å
Source Organism:
Similar Structures:
Biological Unit for 5FZ4: monomeric; determined by author and by software (PISA)
Molecular Components in 5FZ4
Label Count Molecule
Protein (1 molecule)
1
Lysine-specific Demethylase 5B
(Gene symbol: KDM5B)
Molecule annotation
Chemicals and Non-standard biopolymers (19 molecules)
1
2
ZINC IONZINC ION
2
1
(3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol(3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol
3
1
MANGANESE (II) IONMANGANESE (II) ION
4
1
CHLORIDE IONCHLORIDE ION
5
10
1,2-ETHANEDIOL1,2-ETHANEDIOL
6
3
DIMETHYL SULFOXIDEDIMETHYL SULFOXIDE
7
1
PHOSPHATE IONPHOSPHATE ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303