7RV5 | pdb_00007rv5

Crystal structure of the BCL6 BTB domain in complex with OICR-9287

PDB DOI: https://doi.org/10.2210/pdb7RV5/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of the BCL6 BTB domain

Watson, I., Isaac, M.

To be published.

Macromolecule Content

Total Structure Weight: 15.04 kDa
Atom Count: 1,090
Modeled Residue Count: 122
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P41182
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7RB (Subject of Investigation/LOI) Query on 7RB Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[2-(4-benzylpiperidin-1-yl)-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]-N-(3-chloropyridin-4-yl)acetamide C₂₅ H₂₅ Cl N₆ O₂ QBLKKMXYNIFVME-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.62	α = 90
b = 72.198	β = 105.97
c = 55.079	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Canada	--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.