5DKC

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe

• PDB DOI: https://doi.org/10.2210/pdb5DKC/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., Fonseca, M., Krojer, T., Filippakopoulos, P., 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: 1.60 Å
• R-Value Free: 0.211 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe

Tallant, C., Owen, D.R., Gerstenberger, B.S., Fedorov, O., Savitsky, P., Nunez-Alonso, G., Fonseca, M., Krojer, T., Filippakopoulos, P., 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.77 kDa 
• Atom Count: 1,047 
• Modelled Residue Count: 110 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable global transcription activator SNF2L2	A	123	Homo sapiens	Mutation(s): 0  Gene Names: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens) Explore P51531  Go to UniProtKB:  P51531
PHAROS:  P51531 GTEx:  ENSG00000080503

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5BW	C [auth A]	(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	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5BW	BindingDB:  5DKC	Kd: min: 89, max: 100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.211 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.424	α = 90
b = 74.424	β = 90
c = 89.856	γ = 120

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., Fonseca, M., Krojer, T., Filippakopoulos, P., 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