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	LYSINE-SPECIFIC DEMETHYLASE 5B	polymer	479	55214.3	1	UniProt (Q9UGL1) Pfam (PF02375) Pfam (PF02373) Pfam (PF21323) Pfam (PF02928) In PDB	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	A	ZINC ION	non-polymer		65.4	2	Chemie (ZN)
3	A	(3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol	non-polymer		245.3	1	Chemie (P6B)
4	A	MANGANESE (II) ION	non-polymer		54.9	1	Chemie (MN)
5	A	CHLORIDE ION	non-polymer		35.5	1	Chemie (CL)
6	A	1,2-ETHANEDIOL	non-polymer		62.1	10	Chemie (EDO)
7	A	DIMETHYL SULFOXIDE	non-polymer		78.1	3	Chemie (DMS)
8	A	PHOSPHATE ION	non-polymer		95.0	1	Chemie (PO4)
9		water	water		18.0	205	Chemie (HOH)

Sequence modifications

A: 26 - 101 (UniProt: Q9UGL1)

PDB	External Database	Details
Ser -1	-	expression tag
Met 0	-	expression tag

A: 374 - 770 (UniProt: Q9UGL1)

PDB	External Database	Details
Gly 102	-	linker
Gly 103	-	linker
Gly 104	-	linker
Gly 105	-	linker

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

*Water molecules are not included.