6RBI

Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

• PDB DOI: https://doi.org/10.2210/pdb6RBI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-10 Released: 2020-05-13 
• Deposition Author(s): Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.201 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.25 kDa 
• Atom Count: 3,841 
• Modelled Residue Count: 454 
• Deposited Residue Count: 481 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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)
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
JX8 (Subject of Investigation/LOI)	F [auth A]	5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol C10 H7 N5 O COSOIVLLWHGBPW-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.201 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.15	α = 90
b = 142.15	β = 90
c = 151.54	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Johansson, C., Newman, J.A., Kawamura, A., Schofield, C.J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.C.T.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description