5OA0

Crystal structure of mutant AChBP in complex with strychnine (T53F, Q74R, Y110A, I135S, W164F)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein.

Dawson, A.Trumper, P.de Souza, J.O.Parker, H.Jones, M.J.Hales, T.G.Hunter, W.N.

(2019) IUCrJ 6: 1014-1023

  • DOI: https://doi.org/10.1107/S205225251901114X
  • Primary Citation of Related Structures:  
    5O87, 5O8T, 5OA0, 5OAD, 5OAJ, 5OAL, 5OAN, 5OBG

  • PubMed Abstract: 

    Protein-engineering methods have been exploited to produce a surrogate system for the extracellular neurotransmitter-binding site of a heteromeric human ligand-gated ion channel, the glycine receptor. This approach circumvents two major issues: the inherent experimental difficulties in working with a membrane-bound ion channel and the complication that a heteromeric assembly is necessary to create a key, physiologically relevant binding site. Residues that form the orthosteric site in a highly stable ortholog, acetylcholine-binding protein, were selected for substitution. Recombinant proteins were prepared and characterized in stepwise fashion exploiting a range of biophysical techniques, including X-ray crystallography, married to the use of selected chemical probes. The decision making and development of the surrogate, which is termed a glycine-binding protein, are described, and comparisons are provided with wild-type and homomeric systems that establish features of molecular recognition in the binding site and the confidence that the system is suited for use in early-stage drug discovery targeting a heteromeric α/β glycine receptor.


  • Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble acetylcholine receptor
A, B, C, D, E
249Aplysia californicaMutation(s): 5 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Go to UniProtKB:  Q8WSF8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SY9
Query on SY9

Download Ideal Coordinates CCD File 
F [auth A],
N [auth C],
O [auth C],
R [auth D],
U [auth E]
STRYCHNINE
C21 H22 N2 O2
QMGVPVSNSZLJIA-FVWCLLPLSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
K [auth B]
L [auth B]
M [auth B]
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth E],
W [auth E],
X [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.87α = 90
b = 74.87β = 90
c = 185.425γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2020-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary