7F6M | pdb_00007f6m

Crystal structure of APC complexed with a peptide inhibitor MAI-516

• PDB DOI: https://doi.org/10.2210/pdb7F6M/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-25 Released: 2022-06-29 
• Deposition Author(s): Song, K., Zhang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Discovery of Efficient Adenomatous Polyposis Coli - Rho Guanine Nucleotide Exchange Factor 4 Inhibitors by Employing High Binding Affinity Tracer

Jie, Z., 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)

Macromolecule Content 

• Total Structure Weight: 40.9 kDa 
• Atom Count: 2,861 
• Modeled Residue Count: 350 
• Deposited Residue Count: 362 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenomatous polyposis coli protein	A	353	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MAI-516 inhibitor	B	9	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A], K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.751	α = 90
b = 82.337	β = 94.69
c = 49.743	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Song, K., Zhang, J.

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary