2YME

Crystal structure of a mutant binding protein (5HTBP-AChBP) in complex with granisetron


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Ligand Recognition in 5-Ht3 Receptors.

Kesters, D.Thompson, A.J.Brams, M.Van Elk, R.Spurny, R.Geitmann, M.Villalgordo, J.M.Guskov, A.Helena Danielson, U.Lummis, S.C.R.Smit, A.B.Ulens, C.

(2013) EMBO Rep 14: 49

  • DOI: https://doi.org/10.1038/embor.2012.189
  • Primary Citation of Related Structures:  
    2YMD, 2YME

  • PubMed Abstract: 

    The 5-HT(3) receptor is a pentameric serotonin-gated ion channel, which mediates rapid excitatory neurotransmission and is the target of a therapeutically important class of anti-emetic drugs, such as granisetron. We report crystal structures of a binding protein engineered to recognize the agonist serotonin and the antagonist granisetron with affinities comparable to the 5-HT(3) receptor. In the serotonin-bound structure, we observe hydrophilic interactions with loop E-binding site residues, which might enable transitions to channel opening. In the granisetron-bound structure, we observe a critical cation-π interaction between the indazole moiety of the ligand and a cationic centre in loop D, which is uniquely present in the 5-HT(3) receptor. We use a series of chemically tuned granisetron analogues to demonstrate the energetic contribution of this electrostatic interaction to high-affinity ligand binding in the human 5-HT(3) receptor. Our study offers the first structural perspective on recognition of serotonin and antagonism by anti-emetics in the 5-HT(3) receptor.


  • Organizational Affiliation

    Laboratory of Structural Neurobiology, KULeuven, Leuven, Belgium.


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
205Aplysia californicaMutation(s): 1 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CWB
Query on CWB

Download Ideal Coordinates CCD File 
CA [auth H]
FA [auth I]
IA [auth J]
L [auth A]
O [auth B]
CA [auth H],
FA [auth I],
IA [auth J],
L [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
Y [auth F],
Z [auth G]
1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide
C18 H24 N4 O
MFWNKCLOYSRHCJ-BTTYYORXSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth H]
EA [auth I]
HA [auth J]
K [auth A]
N [auth B]
BA [auth H],
EA [auth I],
HA [auth J],
K [auth A],
N [auth B],
P [auth C],
T [auth D],
W [auth E],
X [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth G],
DA [auth H],
M [auth A],
R [auth C],
V [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth I]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CWB Binding MOAD:  2YME Kd: 3.43e+5 (nM) from 1 assay(s)
PDBBind:  2YME Kd: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.09α = 90
b = 138.9β = 91.07
c = 119.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary