5E3D

Crystal structure of the human BRPF1 bromodomain in complex with SEED7

• PDB DOI: https://doi.org/10.2210/pdb5E3D/pdb

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


• Deposited: 2015-10-02 Released: 2016-05-25 
• Deposition Author(s): Zhu, J., Caflisch, A.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.222 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions.

Zhu, J., Caflisch, A.

(2016) J Med Chem 59: 5555-5561

• PubMed: 27167503 
• DOI: https://doi.org/10.1021/acs.jmedchem.6b00215
• Primary Citation of Related Structures:  
  5C7N, 5C85, 5C87, 5DY7, 5DYA, 5DYC, 5E3D, 5E3G, 5EM3, 5EPR, 5EPS, 5EQ1, 5ETB, 5ETD, 5EV9, 5EVA, 5EWC, 5EWD, 5EWH


• PubMed Abstract: 
  

  BRPF1 plays a scaffolding role in transcription. We report on fragment screening by high-throughput docking to the BRPF1 bromodomain which resulted in six chemotypes with very favorable ligand efficiency (0.45-0.50 kcal/mol per non-hydrogen atom). Twenty crystal structures of BRPF1/ligand complexes show structural conservation in the acetyllysine binding site, common binding motifs, and unusual interactions (e.g., the replacement of a conserved water molecule). The structural information is useful for the design of chemical probes.

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Organizational Affiliation: 

Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.

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: 13.97 kDa 
• Atom Count: 1,031 
• Modelled Residue Count: 112 
• 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) Explore P55201  Go to UniProtKB:  P55201
PHAROS:  P55201 GTEx:  ENSG00000156983

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5JL	B [auth A]	2,8-dithioxo-1,2,3,7,8,9-hexahydro-6H-purin-6-one C5 H4 N4 O S2 NDSUZZIWNBVBKW-UHFFFAOYSA-N
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 0.222 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.73	α = 90
b = 60.73	β = 90
c = 62.43	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Zhu, J., Caflisch, A.

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

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-22
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description