7GX0

Crystal Structure of B-cell lymphoma 6 protein BTB domain in complex with ligand 7 at 8.70 MGy X-ray dose.

• PDB DOI: https://doi.org/10.2210/pdb7GX0/pdb
• Deposition Group: G_1002069 ExploreG_1002069

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2024-01-09 Released: 2024-12-11 
• Deposition Author(s): Rodrigues, M.J., Le Bihan, Y.V., van Montfort, R.L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.209 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

Specific radiation damage to halogenated inhibitors and ligands in protein-ligand crystal structures

Rodrigues, M.J., Cabry, M., Collie, G., Carter, M., McAndrew, C., Owen, R.L., Bellenie, B.R., Le Bihan, Y.V., van Montfort, R.L.M.

(2024) J Appl Crystallogr 57: 1951-1965

• DOI: https://doi.org/10.1107/S1600576724010549

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 15.58 kDa 
• Atom Count: 1,363 
• Modelled Residue Count: 130 
• Deposited Residue Count: 134 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma 6 protein	A	128	Homo sapiens	Mutation(s): 0  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WVIP tetrapeptide	B [auth D]	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AB9	C [auth A]	4-chloro-6-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyrimidine-5-carbonitrile C13 H8 Cl N5 O NYUGSENNHNQLPG-UHFFFAOYSA-N
DMS	F [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.209 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.41	α = 90
b = 67.41	β = 90
c = 165.88	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
Aimless	data reduction
BUSTER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Rodrigues, M.J., Le Bihan, Y.V., van Montfort, R.L.M.

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release