5N2L

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue

• PDB DOI: https://doi.org/10.2210/pdb5N2L/pdb

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


• Deposited: 2017-02-07 Released: 2018-02-28 
• Deposition Author(s): Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Wiggers, H.J., Picaud, S., Fedorov, O., Krojer, T., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.233 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue

Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Wiggers, H.J., Picaud, S., Fedorov, O., Krojer, T., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 56.02 kDa 
• Atom Count: 4,074 
• Modelled Residue Count: 433 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C, D	114	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
8J2	H [auth A], L [auth B], O [auth C], P [auth C]	propan-2-yl ~{N}-[(2~{S},4~{R})-6-(3-acetamidophenyl)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate C24 H29 N3 O4 UIHJJMSWZNYBQU-OYHNWAKOSA-N
SO4	E [auth A], I [auth B], J [auth B], K [auth B], M [auth C], Q [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A], G [auth A], N [auth C], R [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.233 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.244	α = 90
b = 94.409	β = 95.43
c = 38.585	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: 2018-02-28 
Deposition Author(s): Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Wiggers, H.J., Picaud, S., Fedorov, O., Krojer, T., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-10-03
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description