5Y2Q | pdb_00005y2q

X-ray structure of acetylcholine binding protein (AChBP) complexed with a small molecule

• PDB DOI: https://doi.org/10.2210/pdb5Y2Q/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Lymnaea stagnalis
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-07-26 Released: 2018-08-08 
• Deposition Author(s): Jiang, L.L., Zhou, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of acetylcholine binding protein (AChBP) complexed with a small molecule

Jiang, L.L., Zhou, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 122.38 kDa 
• Atom Count: 8,252 
• Modeled Residue Count: 999 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine-binding protein	A [auth D], B [auth A], C [auth B], D [auth C], E	212	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154  Go to UniProtKB:  P58154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8L3	F [auth D], G [auth D], H [auth A], I [auth B], J [auth C]	3-[[4-[(3,4-dichlorophenyl)methyl]piperidin-4-yl]methoxy]pyridine C18 H20 Cl2 N2 O DFIMBYYXCVFOEJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
8L3	BindingDB:  5Y2Q	Ki: 72 (nM) from 1 assay(s)
		IC50: 106 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.185	α = 90
b = 77.156	β = 90
c = 222.01	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Jiang, L.L., Zhou, L.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary