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)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | LYSINE-SPECIFIC DEMETHYLASE 5B | polymer | 479 | 55214.3 | 1 | UniProt (Q9UGL1) Pfam (PF02375) Pfam (PF02373) Pfam (PF21323) Pfam (PF02928) | HOMO SAPIENS (HUMAN) | CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA-BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1 |
| 2 | B, C (A) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) | |||
| 3 | D (A) | (3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol | non-polymer | 245.3 | 1 | Chemie (P6B) | |||
| 4 | E (A) | MANGANESE (II) ION | non-polymer | 54.9 | 1 | Chemie (MN) | |||
| 5 | F (A) | CHLORIDE ION | non-polymer | 35.5 | 1 | Chemie (CL) | |||
| 6 | G, H, I, J, K... (A) | 1,2-ETHANEDIOL | non-polymer | 62.1 | 10 | Chemie (EDO) | |||
| 7 | Q, R, S (A) | DIMETHYL SULFOXIDE | non-polymer | 78.1 | 3 | Chemie (DMS) | |||
| 8 | T (A) | PHOSPHATE ION | non-polymer | 95.0 | 1 | Chemie (PO4) | |||
| 9 | U (A) | water | water | 18.0 | 205 | Chemie (HOH) |
Sequence modifications
A: 26 - 101 (UniProt: Q9UGL1)
A: 374 - 770 (UniProt: Q9UGL1)
| PDB | External Database | Details |
|---|---|---|
| Ser -1 | - | expression tag |
| Met 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly 102 | - | linker |
| Gly 103 | - | linker |
| Gly 104 | - | linker |
| Gly 105 | - | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 1 |
| Total formula weight | 55214.3 | |
| Non-Polymers* | Number of molecules | 19 |
| Total formula weight | 1416.5 | |
| All* | Total formula weight | 56630.8 |
