6I81

Crystal Structure of the second bromodomain of BRD2 in complex with RT56

• PDB DOI: https://doi.org/10.2210/pdb6I81/pdb

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


• Deposited: 2018-11-19 Released: 2019-11-27 
• Deposition Author(s): Picaud, S., Traquete, R., Bernardes, G.J.L., Newman, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.196 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Crystal Structure of the second bromodomain of BRD2 in complex with RT56

Picaud, S., Traquete, R., Bernardes, G.J.L., Newman, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

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: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 13.86 kDa 
• Atom Count: 1,060 
• Modelled Residue Count: 110 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A	110	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H7E	D [auth A]	[1-[4-[2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]ethanoylamino]phenyl]piperidin-4-yl]-trimethyl-azanium C34 H39 Cl N7 O2 WDWNSWKCDGLBCQ-PMERELPUSA-O
MES	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.196 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.297	α = 90
b = 127.297	β = 90
c = 40.594	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Picaud, S., Traquete, R., Bernardes, G.J.L., Newman, J., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Filippakopoulos, P., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	095751/Z/11/Z

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description