Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 56.67 kDa 
• Atom Count: 3894 
• Residue Count: 452 
• Unique protein chains: 1

5LWB

Crystal structure of human JARID1B in complex with S40650a

• DOI: 10.2210/pdb5LWB/pdb

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


• Deposited: 2016-09-15 Released: 2016-10-26 
• Deposition Author(s): Srikannathasan, V., Le Bihan, Y.V., Szykowska, A., Johansson, C., Gileadi, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Crystal structure of human JARID1B in complex with S40650a

Srikannathasan, V.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B,Lysine-specific demethylase 5B	A	481	Homo sapiens	Mutation(s): 0  Gene Names: KDM5B, JARID1B, PLU1, RBBP2H1 EC: 1.14.11 (PDB Primary Data), 1.14.11.67 (UniProt)
Find proteins for Q9UGL1 (Homo sapiens) Go to UniProtKB:  Q9UGL1
NIH Common Fund Data Resources
PHAROS  Q9UGL1 GTEx  ENSG00000117139

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
79H	A	5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile C17 H21 N7 O IHWTUDNGWXTJCT-CQSZACIVSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.36	α = 90
b = 142.36	β = 90
c = 151.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-15 
• Released Date: 2016-10-26 
Deposition Author(s): Srikannathasan, V., Le Bihan, Y.V., Szykowska, A., Johansson, C., Gileadi, C., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Oppermann, U., Huber, K.

Revision History 

• Version 1.0: 2016-10-26
  Type: Initial release