6YDV | pdb_00006ydv

Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library

• PDB DOI: https://doi.org/10.2210/pdb6YDV/pdb

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


• Deposited: 2020-03-21 Released: 2020-05-06 
• 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: 2.07 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from 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 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: 86.65 kDa 
• Atom Count: 6,157 
• Modeled Residue Count: 684 
• Deposited Residue Count: 744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
JMJD1B protein	A [auth AAA], B [auth BBB]	372	Homo sapiens	Mutation(s): 0  Gene Names: JMJD1B EC: 1.14.11.65
UniProt
Find proteins for A4FUT8 (Homo sapiens) Explore A4FUT8  Go to UniProtKB:  A4FUT8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ONQ (Subject of Investigation/LOI)	C [auth AAA]	~{N}-(2-azanyl-2-oxidanylidene-ethyl)-4-methoxy-benzamide C10 H12 N2 O3 ZKADLOGPYJUFCB-UHFFFAOYSA-N
MN	H [auth AAA], J [auth BBB]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], I [auth BBB]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.6	α = 90
b = 93.79	β = 107.5
c = 92.61	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-06 
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: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description