5FZM

Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid (N09989b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

• PDB DOI: https://doi.org/10.2210/pdb5FZM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-03-14 Released: 2017-03-29 
• Deposition Author(s): Nowak, R., Krojer, T., Johansson, C., Kupinska, K., Szykowska, A., Pearce, N., Talon, R., Collins, P., Gileadi, C., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., von Delft, F., Brennan, P.E., Oppermann, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.224 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with 3D Fragment 5-(2-Fluorophenyl)-1,3-Oxazole-4-Carboxylic Acid (N09989B) (Ligand Modelled Based on Pandda Event Map, Sgc - Diamond I04-1 Fragment Screening)

Nowak, R., Krojer, T., Johansson, C., Kupinska, K., Szykowska, A., Pearce, N., Talon, R., Collins, P., Gileadi, C., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., von Delft, F., Brennan, P.E., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.46 kDa 
• Atom Count: 3,897 
• Modelled Residue Count: 455 
• Deposited Residue Count: 479 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B	A	479	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGL1 (Homo sapiens) Explore Q9UGL1  Go to UniProtKB:  Q9UGL1
PHAROS:  Q9UGL1 GTEx:  ENSG00000117139

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P60	Q [auth A]	5-(2-fluorophenyl)-1,3-oxazole-4-carboxylic acid C10 H6 F N O3 COYYCXFHTJQGGF-UHFFFAOYSA-N
PO4	S [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS	C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.224 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.88	α = 90
b = 141.88	β = 90
c = 151.61	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
DIMPLE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Nowak, R., Krojer, T., Johansson, C., Kupinska, K., Szykowska, A., Pearce, N., Talon, R., Collins, P., Gileadi, C., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., von Delft, F., Brennan, P.E., Oppermann, U.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description