5OAJ

Crystal structure of mutant AChBP in complex with tropisetron (T53F, Q74R, Y110A, I135S, G162E)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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
A, B, C, D, E, F, G, H, I, J
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TKT (Subject of Investigation/LOI)
Query on TKT

Download Ideal Coordinates CCD File 
CA [auth E],
EB [auth J]
(3-ENDO)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL 1H-INDOLE-3-CARBOXYLATE
C17 H20 N2 O2
ZNRGQMMCGHDTEI-ITGUQSILSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth E],
K [auth A],
SA [auth H],
ZA [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC
Query on FLC

Download Ideal Coordinates CCD File 
NA [auth G],
T [auth C],
XA [auth I]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
AB [auth I]
BA [auth D]
BB [auth I]
CB [auth I]
AA [auth D],
AB [auth I],
BA [auth D],
BB [auth I],
CB [auth I],
DA [auth E],
DB [auth J],
FA [auth E],
FB [auth J],
GA [auth E],
GB [auth J],
HA [auth E],
HB [auth J],
IA [auth F],
IB [auth J],
JA [auth F],
KA [auth F],
L [auth A],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
O [auth B],
OA [auth G],
P [auth B],
PA [auth G],
Q [auth B],
QA [auth G],
R [auth B],
RA [auth G],
S [auth B],
TA [auth H],
U [auth C],
UA [auth H],
V [auth C],
VA [auth H],
W [auth C],
WA [auth H],
X [auth C],
Y [auth D],
YA [auth I],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.239α = 90
b = 137.469β = 90.79
c = 103.666γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2018-09-19
    Changes: Data collection
  • Version 1.2: 2020-02-12
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-10-16
    Changes: Structure summary