5RAU

PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with DA000165b

• PDB DOI: https://doi.org/10.2210/pdb5RAU/pdb
• Deposition Group: G_1002146 (changed state) ExploreG_1002146

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


• Deposited: 2020-03-16 Released: 2020-04-22 
• Deposition Author(s): Snee, M., Nowak, R., Johansson, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.209 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library

Snee, M., Nowak, R., Johansson, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 86.67 kDa 
• Atom Count: 6,278 
• Modelled Residue Count: 684 
• Deposited Residue Count: 744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine-specific demethylase 3B	A, B	372	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HGE (Subject of Investigation/LOI)	C [auth A]	ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate C12 H17 N3 O2 QYHCUDIPSWPYON-UHFFFAOYSA-N
MN	H [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.209 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.68	α = 90
b = 93.8	β = 107.7
c = 93.22	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-22 
Deposition Author(s): Snee, M., Nowak, R., Johansson, C., Burgess-Brown, N.A., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Oppermann, U.

Revision History  

• Version 1.0: 2020-04-22
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references