Macromolecule Content

Total Structure Weight: 53.95 kDa
Atom Count: 3868
Residue Count: 453
Unique protein chains: 1

6EJ0

Crystal structure of KDM5B in complex with KDOPZ000049a.

DOI: 10.2210/pdb6EJ0/pdb

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

Deposited: 2017-09-19 Released: 2018-05-02
Deposition Author(s): Srikannathasan, V., Newman, J.A., Szykowska, A., Wright, M., Ruda, G.F., Vazquez-Rodriguez, S.A., Kupinska, K., Strain-Damerell, C., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A., Bountra, C., Oppermann, U., Huber, K., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.210
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of KDM5B in complex with KDOPZ000049a.

srikannathasan, v.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 5B,Lysine-specific demethylase 5B	A	458	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) Explore Q9UGL1 Go to UniProtKB: Q9UGL1
NIH Common Fund Data Resources
PHAROS: Q9UGL1 GTEx: ENSG00000117139
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B7K Query on B7K Download Ideal Coordinates CCD File SDF format, chain L [A] MOL2 format, chain L [A]	A	7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile C₂₁ H₂₃ N₇ O₂ KGLWYCXNVRPKIE-SFHVURJKSA-N		Ligand Interaction
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [A] SDF format, chain I [A] SDF format, chain J [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [A] MOL2 format, chain J [A]	A	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] MOL2 format, chain D [A] MOL2 format, chain E [A]	A	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain K [A] MOL2 format, chain C [A] MOL2 format, chain K [A]	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.210
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.82	α = 90
b = 141.82	β = 90
c = 151.75	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2017-09-19
Released Date: 2018-05-02

Deposition Author(s):

Srikannathasan, V.

Vazquez-Rodriguez, S.A.

Strain-Damerell, C.

Burgess-Brown, N.A.

Arrowsmith, C.H.

Revision History

Version 1.0: 2018-05-02
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.