Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 53.94 kDa 
• Atom Count: 3882 
• Residue Count: 451 
• Unique protein chains: 1

6EK6

Crystal structure of KDM5B in complex with S49195a.

• DOI: 10.2210/pdb6EK6/pdb

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


• Deposited: 2017-09-25 Released: 2018-03-14 
• Deposition Author(s): Srikannathasan, V., Szykowska, A., Newman, J.A., Ruda, G.F., Strain-Damerell, C., Burgess-Brown, N.A., Vazquez-Rodriguez, S., Wright, M., Brennan, P.E., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Huber, K., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.200 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Crystal structure of KDM5B in complex with S49195a.

Srikannathasan, V.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B	A	455	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
90V	A	N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide C15 H22 N4 O2 CXEXTVGTDZRKJS-LLVKDONJSA-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
NI	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MN	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.200 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.41	α = 90
b = 141.41	β = 90
c = 150.95	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: 2017-09-25 
• Released Date: 2018-03-14 
Deposition Author(s): Srikannathasan, V., Szykowska, A., Newman, J.A., Ruda, G.F., Strain-Damerell, C., Burgess-Brown, N.A., Vazquez-Rodriguez, S., Wright, M., Brennan, P.E., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Huber, K., von Delft, F.

Revision History 

• Version 1.0: 2018-03-14
  Type: Initial release