5DKD | pdb_00005dkd

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe

• PDB DOI: https://doi.org/10.2210/pdb5DKD/pdb

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


• Deposited: 2015-09-03 Released: 2015-10-14 
• Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Newman, J.A., Filippakopoulos, P., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.297 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human BRG1 (SMARCA4) in complex with PFI-3 chemical probe

Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Newman, J.A., Filippakopoulos, P., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., 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: 29.61 kDa 
• Atom Count: 2,002 
• Modeled Residue Count: 220 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription activator BRG1	A, B	121	Homo sapiens	Mutation(s): 0  Gene Names: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51532 (Homo sapiens) Explore P51532  Go to UniProtKB:  P51532
PHAROS:  P51532 GTEx:  ENSG00000127616

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5BW	G [auth A], L [auth B]	(2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one C19 H19 N3 O2 INAICWLVUAKEPB-QSTFCLMHSA-N
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5BW	BindingDB:  5DKD	Kd: min: 21, max: 9.70e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.297 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.926	α = 90
b = 74.566	β = 109.9
c = 52.626	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: 2015-10-14 
Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Newman, J.A., Filippakopoulos, P., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Knapp, S.

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description