5FG6 | pdb_00005fg6

Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 chemical probe

• PDB DOI: https://doi.org/10.2210/pdb5FG6/pdb

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


• Deposited: 2015-12-20 Released: 2016-02-03 
• 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., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the bromodomain of human BRD1 (BRPF2) in complex with OF-1 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., Bountra, C., Muller, S., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.7 kDa 
• Atom Count: 1,229 
• Modeled Residue Count: 118 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 1	A	128	Homo sapiens	Mutation(s): 0  Gene Names: BRD1, BRL, BRPF2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens) Explore O95696  Go to UniProtKB:  O95696
PHAROS:  O95696 GTEx:  ENSG00000100425

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5XE	F [auth A]	4-bromanyl-~{N}-(6-methoxy-1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)-2-methyl-benzenesulfonamide C17 H18 Br N3 O4 S YUNQZQREIHWDQT-UHFFFAOYSA-N
PO4	H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	G [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.771	α = 90
b = 84.328	β = 90
c = 52.08	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: 2016-02-03 
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., Knapp, S.

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 2.0: 2024-01-10
  Changes: Atomic model, Data collection, Database references, Refinement description