5OBG | pdb_00005obg

Crystal structure of glycine binding protein in complex with strychnine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.250 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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: 146.68 kDa 
  • Atom Count: 9,478 
  • Modeled Residue Count: 1,038 
  • Deposited Residue Count: 1,245 
  • 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
249Aplysia californicaMutation(s): 9 
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
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SY9
(Subject of Investigation/LOI)

Query on SY9



Download:Ideal Coordinates CCD File
CA [auth C],
F [auth A],
LA [auth D],
Q [auth B],
XA [auth E]
STRYCHNINE
C21 H22 N2 O2
QMGVPVSNSZLJIA-FVWCLLPLSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
DA [auth C],
MA [auth D],
R [auth B],
YA [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth C]
BB [auth E]
CB [auth E]
DB [auth E]
EA [auth C]
BA [auth C],
BB [auth E],
CB [auth E],
DB [auth E],
EA [auth C],
EB [auth E],
FA [auth C],
FB [auth E],
G [auth A],
GA [auth C],
GB [auth E],
H [auth A],
HA [auth C],
I [auth A],
J [auth A],
KA [auth C],
M [auth A],
N [auth A],
OA [auth D],
P [auth A],
PA [auth D],
QA [auth D],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
U [auth B],
V [auth B],
WA [auth E],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth E]
JA [auth C]
L [auth A]
NA [auth D]
AA [auth C],
AB [auth E],
JA [auth C],
L [auth A],
NA [auth D],
O [auth A],
VA [auth E],
X [auth B],
ZA [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
IA [auth C],
K [auth A],
TA [auth D],
UA [auth E],
W [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.250 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.353α = 90
b = 100.04β = 90
c = 163.752γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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
  • Version 1.4: 2024-11-06
    Changes: Structure summary