6RBJ | pdb_00006rbj

Crystal structure of KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

• PDB DOI: https://doi.org/10.2210/pdb6RBJ/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.210 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of KDM3B 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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.93 kDa 
• Atom Count: 5,561 
• Modeled Residue Count: 676 
• Deposited Residue Count: 702 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 3B	A, B	351	Homo sapiens	Mutation(s): 0  Gene Names: KDM3B, C5orf7, JHDM2B, JMJD1B, KIAA1082 EC: 1.14.11 (PDB Primary Data), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7LBC6 (Homo sapiens) Explore Q7LBC6  Go to UniProtKB:  Q7LBC6
PHAROS:  Q7LBC6 GTEx:  ENSG00000120733

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JX8 (Subject of Investigation/LOI)	E [auth A], K [auth B]	5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol C10 H7 N5 O COSOIVLLWHGBPW-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	F [auth A], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.210 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.929	α = 90
b = 93.754	β = 107.29
c = 90.494	γ = 90

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