5HEM | pdb_00005hem

Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2

• PDB DOI: https://doi.org/10.2210/pdb5HEM/pdb

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


• Deposited: 2016-01-06 Released: 2016-01-20 
• Deposition Author(s): Tallant, C., Lori, C., Pasquo, A., Chiaraluce, R., Consalvi, V., Newman, J.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.199 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the N-terminus D161Y bromodomain mutant of human BRD2

Tallant, C., Lori, C., Pasquo, A., Chiaraluce, R., Consalvi, V., Newman, J.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.38 kDa 
• Atom Count: 2,225 
• Modeled Residue Count: 237 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B	126	Homo sapiens	Mutation(s): 1  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
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	H [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.199 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.73	α = 90
b = 68.73	β = 90
c = 113.364	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Tallant, C., Lori, C., Pasquo, A., Chiaraluce, R., Consalvi, V., Newman, J.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description