2DVV | pdb_00002dvv

Crystal structure of the second bromodomain of the human Brd2 protein

• PDB DOI: https://doi.org/10.2210/pdb2DVV/pdb

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


• Deposited: 2006-08-01 Released: 2007-08-07 
• Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.188 (Depositor) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the second bromodomain of the human Brd2 protein

Padmanabhan, B., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.42 kDa 
• Atom Count: 1,198 
• Modeled Residue Count: 112 
• Deposited Residue Count: 112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A	112	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.188 (Depositor) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.782	α = 90
b = 52.604	β = 90
c = 32.059	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-07 
Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-08-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description