5FZH

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4,5-dihydronaphtho(1,2-b)thiophene-2- carboxylicacid (N11181a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening)

• PDB DOI: https://doi.org/10.2210/pdb5FZH/pdb

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


• Deposited: 2016-03-14 Released: 2016-05-25 
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.222 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Maybridge Fragment 4,5-Dihydronaphtho(1,2-B)Thiophene-2-Carboxylicacid (N11181A) (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: 56.62 kDa 
• Atom Count: 4,087 
• Modelled Residue Count: 460 
• Deposited Residue Count: 479 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
0TI	R [auth A]	(3R)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one C8 H6 F N O2 XYDTZHMQTYEJQN-SSDOTTSWSA-N
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	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], S [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	Q [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.222 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.13	α = 90
b = 144.13	β = 90
c = 154.16	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: 2016-05-25 
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: 2016-05-25
  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