5FG5

Crystal structure of the bromodomain of human BRPF1 in complex with PFI-4 chemical probe

• PDB DOI: https://doi.org/10.2210/pdb5FG5/pdb

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


• Deposited: 2015-12-20 Released: 2015-12-30 
• Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Savitsky, P., Chaikuad, A., Fedorov, O., Nunez-Alonso, G., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Brennan, P.E., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human BRPF1 in complex with PFI-4 chemical probe

Tallant, C., Owen, D.R., Gerstenberger, B.S., Savitsky, P., Chaikuad, A., Fedorov, O., Nunez-Alonso, G., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Brennan, P.E., 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: 28.23 kDa 
• Atom Count: 2,183 
• Modelled Residue Count: 222 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peregrin	A, B	116	Homo sapiens	Mutation(s): 0  Gene Names: BRPF1, BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201  Go to UniProtKB:  P55201
PHAROS:  P55201 GTEx:  ENSG00000156983

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5XF	C [auth A], E [auth B]	~{N}-(1,3-dimethyl-2-oxidanylidene-6-pyrrolidin-1-yl-benzimidazol-5-yl)-2-methoxy-benzamide C21 H24 N4 O3 QCIJLRJBZDBVDB-UHFFFAOYSA-N
NO3	D [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.919	α = 90
b = 68.141	β = 94.33
c = 72.656	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: 2015-12-30 
Deposition Author(s): Tallant, C., Owen, D.R., Gerstenberger, B.S., Savitsky, P., Chaikuad, A., Fedorov, O., Nunez-Alonso, G., Filippakopoulos, P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Muller, S., Brennan, P.E., Knapp, S.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description