7RV6 | pdb_00007rv6

Crystal structure of the BCL6 BTB domain in complex with OICR-9288

• PDB DOI: https://doi.org/10.2210/pdb7RV6/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2021-08-18 Released: 2022-08-24 
• Deposition Author(s): Kuntz, D.A., Prive, G.G.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Structure of the BCL6 BTB domain

Watson, I., Isaac, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 15.15 kDa 
• Atom Count: 1,154 
• Modeled Residue Count: 123 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of B-cell lymphoma 6 protein	A	127	Homo sapiens	Mutation(s): 3  Gene Names: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
UniProt & NIH Common Fund Data Resources
Find proteins for P41182 (Homo sapiens) Explore P41182  Go to UniProtKB:  P41182
PHAROS:  P41182 GTEx:  ENSG00000113916

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7SC (Subject of Investigation/LOI)	B [auth A]	N-(3-chloropyridin-4-yl)-2-{4-oxo-2-[(2-phenylethyl)amino]-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide C21 H19 Cl N6 O2 PYOLWRAPHCCKEJ-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.339	α = 90
b = 72.177	β = 106.26
c = 54.811	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Kuntz, D.A., Prive, G.G.

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Funding Organization	Location	Grant Number
Other government	Canada	--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description