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
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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
Modelled 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.