5QXM

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF789

• PDB DOI: https://doi.org/10.2210/pdb5QXM/pdb
• Deposition Group: G_1002118 (changed state) ExploreG_1002118

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


• Deposited: 2020-02-11 Released: 2020-04-08 
• Deposition Author(s): Snee, M., Talon, R., Fowley, D., Collins, P., Nelson, A., Arrowsmith, C.H., Bountra, C., Edwards, A., Von-Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.179 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

PanDDA analysis group deposition - Bromodomain of human ATAD2 fragment screening

Snee, M., Talon, R., Fowley, D., Collins, P., Nelson, A., Arrowsmith, C.H., Bountra, C., Edwards, A., Von-Delft, F.

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)

Macromolecule Content

• Total Structure Weight: 16.34 kDa 
• Atom Count: 1,494 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPase family AAA domain-containing protein 2	A	130	Homo sapiens	Mutation(s): 0  Gene Names: ATAD2, L16, PRO2000 EC: 3.6.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PL18 (Homo sapiens) Explore Q6PL18  Go to UniProtKB:  Q6PL18
PHAROS:  Q6PL18 GTEx:  ENSG00000156802

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RHJ (Subject of Investigation/LOI)	G [auth A]	cyclobutyl[(3aS,4R,5R,7S,8aS)-4,5-dihydroxyhexahydro-1H-3a,7-epoxycyclohepta[c]pyrrol-2(3H)-yl]methanone C14 H21 N O4 BYVLFJJVWOHEND-JCCXBDGPSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.179 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.769	α = 90
b = 80.769	β = 90
c = 140.797	γ = 120

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: 2020-04-08 
Deposition Author(s): Snee, M., Talon, R., Fowley, D., Collins, P., Nelson, A., Arrowsmith, C.H., Bountra, C., Edwards, A., Von-Delft, F.

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 2.0: 2023-05-31
  Changes: Database references, Derived calculations, Non-polymer description, Structure summary