5O87 | pdb_00005o87

Crystal structure of wild type Aplysia californica AChBP in complex with nicotine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.235 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5O87

Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 292.21 kDa 
  • Atom Count: 18,900 
  • Modeled Residue Count: 2,065 
  • Deposited Residue Count: 2,490 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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): 0 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
EA [auth C]
GB [auth F]
HC [auth I]
L [auth A]
NA [auth D]
EA [auth C],
GB [auth F],
HC [auth I],
L [auth A],
NA [auth D],
QB [auth G],
RC [auth J],
U [auth B],
XA [auth E],
ZB [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NCT
(Subject of Investigation/LOI)

Query on NCT



Download:Ideal Coordinates CCD File
DA [auth C]
FB [auth F]
GC [auth I]
K [auth A]
MA [auth D]
DA [auth C],
FB [auth F],
GC [auth I],
K [auth A],
MA [auth D],
PB [auth G],
QC [auth J],
T [auth B],
WA [auth E],
YB [auth H]
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
C10 H14 N2
SNICXCGAKADSCV-JTQLQIEISA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
AB [auth E]
BB [auth E]
BC [auth H]
CC [auth H]
HA [auth C]
AB [auth E],
BB [auth E],
BC [auth H],
CC [auth H],
HA [auth C],
IA [auth C],
JB [auth F],
KB [auth F],
KC [auth I],
LC [auth I],
O [auth A],
P [auth A],
QA [auth D],
RA [auth D],
TB [auth G],
UB [auth G],
UC [auth J],
VC [auth J],
X [auth B],
Y [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth B]
AC [auth H]
BA [auth B]
CB [auth E]
DB [auth E]
AA [auth B],
AC [auth H],
BA [auth B],
CB [auth E],
DB [auth E],
DC [auth H],
EC [auth H],
FA [auth C],
GA [auth C],
HB [auth F],
IB [auth F],
IC [auth I],
JA [auth C],
JC [auth I],
KA [auth C],
LB [auth F],
M [auth A],
MB [auth F],
MC [auth I],
N [auth A],
NB [auth F],
NC [auth I],
OA [auth D],
OC [auth I],
PA [auth D],
Q [auth A],
R [auth A],
RB [auth G],
SA [auth D],
SB [auth G],
SC [auth J],
TA [auth D],
TC [auth J],
UA [auth D],
V [auth B],
VB [auth G],
W [auth B],
WB [auth G],
WC [auth J],
YA [auth E],
Z [auth B],
ZA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
CA [auth B]
EB [auth E]
FC [auth H]
LA [auth C]
OB [auth F]
CA [auth B],
EB [auth E],
FC [auth H],
LA [auth C],
OB [auth F],
PC [auth I],
S [auth A],
VA [auth D],
XB [auth G],
XC [auth J]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.235 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.781α = 90
b = 131.999β = 103.15
c = 130.655γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    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
  • Version 1.4: 2024-10-23
    Changes: Structure summary