5FZ1 | pdb_00005fz1

Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 2,4-dichloro-N-pyridin-3-ylbenzamide (E48115b) (ligand modelled based on PANDDA event map)

• PDB DOI: https://doi.org/10.2210/pdb5FZ1/pdb

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


• Deposited: 2016-03-10 Released: 2016-05-04 
• Deposition Author(s): Nowak, R., Krojer, T., Johansson, C., Gileadi, C., Kupinska, K., Strain-Damerell, C., Szykowska, A., 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: 2.39 Å
• R-Value Free: 
  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with E48115B

Nowak, R., Krojer, T., Johansson, C., Pearce, N., Gileadi, C., Kupinska, K., Strain-Damerell, C., Szykowska, A., 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: 56.74 kDa 
• Atom Count: 4,007 
• Modeled Residue Count: 454 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W77	U [auth A]	2,4-dichloro-N-(pyridin-3-yl)benzamide C12 H8 Cl2 N2 O RQQYPUUCNNBJEH-UHFFFAOYSA-N
PO4	H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS	D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	G [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.222 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.3	α = 90
b = 143.3	β = 90
c = 152.89	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: 2016-05-04 
Deposition Author(s): Nowak, R., Krojer, T., Johansson, C., Gileadi, C., Kupinska, K., Strain-Damerell, C., Szykowska, A., 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: 2016-05-04
  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