4QSW | pdb_00004qsw

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 5-methyl uridine

• PDB DOI: https://doi.org/10.2210/pdb4QSW/pdb

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


• Deposited: 2014-07-06 Released: 2014-07-23 
• Deposition Author(s): Chaikuad, A., Felletar, I., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain

Chaikuad, A., Petros, A.M., Fedorov, O., Xu, J., Knapp, S.

(2014) Medchemcomm 5: 1843-1848

• DOI: https://doi.org/10.1039/C4MD00237G

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: 1,434 
• 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
38T	H [auth A]	5-methyluridine C10 H14 N2 O6 DWRXFEITVBNRMK-JXOAFFINSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.59	α = 90
b = 79.59	β = 90
c = 138.421	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-23 
Deposition Author(s): Chaikuad, A., Felletar, I., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description