5OWB

Crystal structure of the human BRPF1 bromodomain in complex with DSPBP1004

• PDB DOI: https://doi.org/10.2210/pdb5OWB/pdb

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


• Deposited: 2017-08-31 Released: 2018-07-18 
• Deposition Author(s): Zhu, J., Spiliotopoulos, D., Caflisch, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Crystal structure of the human BRPF1 bromodomain in complex with DSPBP1004

Zhu, J., Caflisch, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.93 kDa 
• Atom Count: 1,135 
• 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
AYW	C [auth A]	4-methyl-6-oxidanyl-1-benzofuran-3-one C9 H8 O3 JANZWCJQQFVOPT-UHFFFAOYSA-N
NO3	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.204 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.426	α = 90
b = 60.426	β = 90
c = 63.468	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Zhu, J., Spiliotopoulos, D., Caflisch, A.

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description