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.

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

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of KDM5B in complex with S49195a.

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	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) Explore Q9UGL1 Go to UniProtKB: Q9UGL1
NIH Common Fund Data Resources
PHAROS: Q9UGL1 GTEx: ENSG00000117139
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
90V Query on 90V Download Ideal Coordinates CCD File SDF format, chain E [A] MOL2 format, chain E [A]	A	N-{(3R)-1-[3-(propan-2-yl)-1H-pyrazole-5-carbonyl]pyrrolidin-3-yl}cyclopropanecarboxamide C₁₅ H₂₂ N₄ O₂ CXEXTVGTDZRKJS-LLVKDONJSA-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] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [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 J [A] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain M [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain P [A] MOL2 format, chain J [A] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain M [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain P [A]	A	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain D [A] MOL2 format, chain D [A]	A	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Ligand Interaction
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain C [A] MOL2 format, chain C [A]	A	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2017-09-25
Released Date: 2018-03-14

Deposition Author(s):

Srikannathasan, V.

Strain-Damerell, C.

Burgess-Brown, N.A.

Vazquez-Rodriguez, S.

Arrowsmith, C.H.

Revision History

Version 1.0: 2018-03-14
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.