5EPB | pdb_00005epb

Crystal structure of the bromodomain of human ATAD2 in complex with Compound 49

• PDB DOI: https://doi.org/10.2210/pdb5EPB/pdb

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


• Deposited: 2015-11-11 Released: 2016-11-23 
• Deposition Author(s): Dong, J., Caflisch, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human ATAD2 in complex with Compound 49

Dong, J., Caflisch, A.

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: 16.25 kDa 
• Atom Count: 1,369 
• 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
5QW	B [auth A], C [auth A]	~{N}-[(2~{S})-2-morpholin-4-ylpropyl]-4-oxidanylidene-3,5-dihydro-2~{H}-1,5-benzothiazepine-7-carboxamide C17 H23 N3 O3 S MNYMDWGPOVDYSU-LBPRGKRZSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.258	α = 90
b = 79.258	β = 90
c = 139.121	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Dong, J., Caflisch, A.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description