4D6S: crystal structure of human JMJD2D in complex with N-OXALYLGLYCINE and bound 5,6-Dimethylbenzimidazole

PDB ID: 4D6SDownload
MMDB ID: 150241
PDB Deposition Date: 2014/11/14
Updated in MMDB: 2024/05
Experimental Method:
x-ray diffraction
Resolution: 1.4  Å
Source Organism:
Similar Structures:
Biological Unit for 4D6S: monomeric; determined by author and by software (PISA)
Molecular Components in 4D6S
Label Count Molecule
Protein (1 molecule)
1
Lysine-specific Demethylase 4D
(Gene symbol: KDM4D)
Molecule annotation
Chemicals and Non-standard biopolymers (16 molecules)
1
1
ZINC IONZINC ION
2
1
NICKEL (II) IONNICKEL (II) ION
3
1
5,6-DIMETHYLBENZIMIDAZOLE5,6-DIMETHYLBENZIMIDAZOLE
4
1
N-OXALYLGLYCINEN-OXALYLGLYCINE
5
10
1,2-ETHANEDIOL1,2-ETHANEDIOL
6
1
DIMETHYL SULFOXIDEDIMETHYL SULFOXIDE
7
1
SULFATE IONSULFATE 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