7F7O

APC-Asef FP assay tracer

• PDB DOI: https://doi.org/10.2210/pdb7F7O/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-30 Released: 2022-07-06 
• Deposition Author(s): Yang, X., Zhang, J.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.328 
• R-Value Work: 0.285 
• R-Value Observed: 0.287 

Starting Model: experimental

Literature

The tracer of FP assay for screening APC-Asef inhbitors

Yang, X., Zhang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content

• Total Structure Weight: 38.71 kDa 
• Atom Count: 2,647 
• Modelled Residue Count: 335 
• Deposited Residue Count: 345 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenomatous polyposis coli protein	A	335	Homo sapiens	Mutation(s): 0  Gene Names: APC, DP2.5
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054  Go to UniProtKB:  P25054
GTEx:  ENSG00000134982

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tracer 7	B	10	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4CI (Subject of Investigation/LOI)	C [auth B]	N-[3',6'-bis(oxidanyl)-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-5-yl]methanethioamide C21 H13 N O5 S XXJHFVNZDWPRIR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.328 
• R-Value Work: 0.285 
• R-Value Observed: 0.287 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.234	α = 90
b = 71.619	β = 90
c = 83.873	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Yang, X., Zhang, J.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description