1X0J | pdb_00001x0j

Crystal structure analysis of the N-terminal bromodomain of human Brd2

• PDB DOI: https://doi.org/10.2210/pdb1X0J/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-03-23 Released: 2006-06-27 
• Deposition Author(s): Nakamura, Y., Umehara, T., Shirouzu, M., 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: 
  0.213 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structural basis for acetylated histone H4 recognition by the human Brd2 bromodomain

Nakamura, Y., Umehara, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.06 kDa 
• Atom Count: 3,171 
• Modeled Residue Count: 333 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C	122	Homo sapiens	Mutation(s): 7
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
MES	G [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
DTT	D [auth A], E [auth B], F [auth C]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.397	α = 90
b = 55.363	β = 94.07
c = 67.584	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-27 
Deposition Author(s): Nakamura, Y., Umehara, T., Shirouzu, M., Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary