7BLC

BAZ2A bromodomain in complex with compound UP39

• PDB DOI: https://doi.org/10.2210/pdb7BLC/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-18 Released: 2022-03-02 
• Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Caflisch, A., Lolli, G.
• Funding Organization(s): Italian Association for Cancer Research, Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.217 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Chemical probes in the BAZ2A bromodomain

Cazzanelli, G., Dalle Vedove, A., D'Agostino, V.G., Caflisch, A., Lolli, G.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.32 kDa 
• Atom Count: 959 
• Modelled Residue Count: 102 
• Deposited Residue Count: 105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain adjacent to zinc finger domain protein 2A	A	105	Homo sapiens	Mutation(s): 0  Gene Names: BAZ2A, KIAA0314, TIP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIF9 (Homo sapiens) Explore Q9UIF9  Go to UniProtKB:  Q9UIF9
PHAROS:  Q9UIF9 GTEx:  ENSG00000076108

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U2E (Subject of Investigation/LOI)	B [auth A], C [auth A]	methyl 5-[(5-ethanoyl-2-ethoxy-phenyl)carbamoyl]-2-(2-piperazin-1-ylethoxy)benzoate C25 H31 N3 O6 LQHWWGHAUAZICR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.217 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.95	α = 90
b = 94.95	β = 90
c = 32.355	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
Aimless	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Dalle Vedove, A., Cazzanelli, G., Caflisch, A., Lolli, G.

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Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	MFAG 2017 - ID. 19882
Swiss National Science Foundation	Switzerland	SNSF grant 310030B-189363

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description