7RV8 | pdb_00007rv8

Crystal structure of the BCL6 BTB domain in complex with OICR-10268

PDB DOI: https://doi.org/10.2210/pdb7RV8/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: 1.25 Å
R-Value Free:
0.162 (Depositor), 0.164 (DCC)
R-Value Work:
0.137 (Depositor), 0.138 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structure of the BCL6 BTB domain

Watson, I., Isaac, M.

To be published.

Macromolecule Content

Total Structure Weight: 15.28 kDa
Atom Count: 1,169
Modeled Residue Count: 122
Deposited Residue Count: 127
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41182
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7ST (Subject of Investigation/LOI) Query on 7ST 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]	N-[5-chloro-2-(morpholin-4-yl)pyridin-4-yl]-2-{5-(3-cyano-4-hydroxy-5-methylphenyl)-3-[3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl]-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide C₃₂ H₂₈ Cl N₉ O₄ GOJWPRIJLIIWBN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.162 (Depositor), 0.164 (DCC)
R-Value Work: 0.137 (Depositor), 0.138 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.768	α = 90
b = 72.566	β = 105.85
c = 55.128	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-04-03
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.