5QXX | pdb_00005qxx

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with RZ99

• PDB DOI: https://doi.org/10.2210/pdb5QXX/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: 1.58 Å
• R-Value Free: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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: 16.12 kDa 
• Atom Count: 1,497 
• Modeled 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 (PDB Primary Data), 3.6.1 (UniProt)
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
RK1 (Subject of Investigation/LOI)	B [auth A]	(7R)-N-benzyl-1,7-diethyl-2,3,6,7-tetrahydro-1H-1,4-diazepine-7-carboxamide C17 H25 N3 O ZQBDTUTZFRWAGO-QGZVFWFLSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.223	α = 90
b = 80.223	β = 90
c = 139.288	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 1.1: 2024-03-06
  Changes: Data collection, Database references