6EPX | pdb_00006epx

The ATAD2 bromodomain in complex with compound 3

• PDB DOI: https://doi.org/10.2210/pdb6EPX/pdb

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


• Deposited: 2017-10-12 Released: 2018-10-31 
• Deposition Author(s): Sledz, P., Caflisch, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers.

Dolbois, A., Batiste, L., Wiedmer, L., Dong, J., Brutsch, M., Huang, D., Deerain, N.M., Spiliotopoulos, D., Cheng-Sanchez, I., Laul, E., Nevado, C., Sledz, P., Caflisch, A.

(2020) ACS Med Chem Lett 11: 1573-1580

• PubMed: 32832026 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00080
• Primary Citation Related Structures: 
  5F36, 6EPJ, 6EPT, 6EPU, 6EPV, 6EPX, 6HI3, 6HI4, 6HI5, 6HI6, 6HI7, 6HI8, 6HIA, 6HIB, 6HIC, 6HID, 6HIE


• PubMed Abstract: 
  

  Small molecule ligand binding to the ATAD2 bromodomain is investigated here through the synergistic combination of molecular dynamics and protein crystallography. A previously unexplored conformation of the binding pocket upon rearrangement of the gatekeeper residue Ile1074 has been found. Further, our investigations reveal how minor structural differences in the ligands result in binding with different plasticity of the ZA loop for this difficult-to-drug bromodomain.

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Organizational Affiliation: 
• Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.07 kDa 
• Atom Count: 1,222 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BQW (Subject of Investigation/LOI)	B [auth A], C [auth A]	(2~{R})-2-carbamimidamido-~{N}-(4-ethanoyl-1,3-thiazolidin-2-yl)propanamide C9 H17 N5 O2 S LAWADVQORXPDOH-VKJXWFFISA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.575	α = 90
b = 79.575	β = 90
c = 138.187	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-31 
Deposition Author(s): Sledz, P., Caflisch, A.

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Data collection, Database references
• Version 1.2: 2020-11-04
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references