7UU0 | pdb_00007uu0

Crystal structure of the BRD2-BD2 in complex with a ligand

• PDB DOI: https://doi.org/10.2210/pdb7UU0/pdb

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


• Deposited: 2022-04-28 Released: 2023-05-03 
• Deposition Author(s): Kalra, P., Shi, K., Aihara, H., Pomerantz, W.C.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Library of Medicine (NIH/NLM)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal structure of the BRD2-BD2 in complex with a ligand

Kalra, P., Shi, K., Aihara, H., Pomerantz, W.C.K.

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: 16.17 kDa 
• Atom Count: 1,227 
• Modeled Residue Count: 113 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 3 of Bromodomain-containing protein 2	A	135	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QJ1	C [auth A]	methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate C11 H15 N O2 S2 GTUMUZDXWXZZSA-JTQLQIEISA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.309	α = 90
b = 52.526	β = 90
c = 71.216	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Kalra, P., Shi, K., Aihara, H., Pomerantz, W.C.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM118047
National Institutes of Health/National Library of Medicine (NIH/NLM)	United States	5T32GM008347-23

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection