5R4X

XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13413a

• PDB DOI: https://doi.org/10.2210/pdb5R4X/pdb
• Deposition Group: G_1002130 (changed state) ExploreG_1002130

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


• Deposited: 2020-02-28 Released: 2020-05-13 
• Deposition Author(s): Talon, R., Krojer, T., Fairhead, M., Sethi, R., Bradley, A.R., Aimon, A., Collins, P., Brandao-Neto, J., Douangamath, A., Wright, N., MacLean, E., Zhang, R., Dias, A., Brennan, P.E., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.159 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Literature

XChem fragment screen

Talon, R., Krojer, T., Fairhead, M., Sethi, R., Bradley, A.R., Aimon, A., Collins, P., Brandao-Neto, J., Douangamath, A., Wright, N., MacLean, E., Zhang, R., Dias, A., Brennan, P.E., Bountra, C., Arrowsmith, C.H., 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: 16.15 kDa 
• Atom Count: 1,409 
• 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 (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
K3D (Subject of Investigation/LOI)	B [auth A]	4-acetyl-N-ethylpiperazine-1-carboxamide C9 H17 N3 O2 DXJHUMXFQJQTMZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.159 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.79	α = 90
b = 80.79	β = 90
c = 140.36	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: 2020-05-13 
Deposition Author(s): Talon, R., Krojer, T., Fairhead, M., Sethi, R., Bradley, A.R., Aimon, A., Collins, P., Brandao-Neto, J., Douangamath, A., Wright, N., MacLean, E., Zhang, R., Dias, A., Brennan, P.E., Bountra, C., Arrowsmith, C.H., Edwards, A., von Delft, F.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references