7F7O | pdb_00007f7o

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 (Depositor), 0.320 (DCC)
R-Value Work:
0.285 (Depositor), 0.280 (DCC)
R-Value Observed:
0.287 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The tracer of FP assay for screening APC-Asef inhbitors

Yang, X., Zhang, J.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
PHAROS: P25054 GTEx: ENSG00000134982
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25054
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tracer 7	B	10	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4CI (Subject of Investigation/LOI) Query on 4CI Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	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		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.328 (Depositor), 0.320 (DCC)
R-Value Work: 0.285 (Depositor), 0.280 (DCC)
R-Value Observed: 0.287 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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.