5EWW

Crystal structure of the human BRPF1 bromodomain in complex with SEED21

• PDB DOI: https://doi.org/10.2210/pdb5EWW/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-21 Released: 2016-11-02 
• Deposition Author(s): Zhu, J., Wiedmer, L., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

Crystal structure of the human BRPF1 bromodomain in complex with SEED21

Zhu, J., Wiedmer, L., Caflisch, A.

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: 14.02 kDa 
• Atom Count: 1,079 
• Modelled Residue Count: 113 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5SK	B [auth A]	~{N}-[(2~{R})-butan-2-yl]-1-methyl-[1,2,4]triazolo[4,3-a]quinoxalin-4-amine C14 H17 N5 NPOOPJOEQAWGNZ-SECBINFHSA-N
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.52	α = 90
b = 60.52	β = 90
c = 62.92	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Zhu, J., Wiedmer, L., Caflisch, A.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Atomic model, Data collection, Database references, Refinement description