2YMD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural Basis of Ligand Recognition in 5-Ht(3) 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.Smit, A.B.Ulens, C.

(2013) EMBO Rep 14: 49

  • DOI: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
212Aplysia californicaMutation(s): 1 
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SRO (Subject of Investigation/LOI)
Query on SRO

Download Ideal Coordinates CCD File 
AA [auth E] , EA [auth F] , IA [auth G] , K [auth A] , LA [auth H] , NA [auth I] , O [auth B] , PA [auth J] , 
AA [auth E], EA [auth F], IA [auth G], K [auth A], LA [auth H], NA [auth I], O [auth B], PA [auth J], S [auth C], W [auth D]
SEROTONIN
C10 H12 N2 O
QZAYGJVTTNCVMB-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
CA [auth E] , GA [auth F] , JA [auth G] , M [auth A] , MA [auth H] , OA [auth I] , Q [auth B] , QA [auth J] , 
CA [auth E], GA [auth F], JA [auth G], M [auth A], MA [auth H], OA [auth I], Q [auth B], QA [auth J], U [auth C], Z [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth E] , DA [auth F] , FA [auth F] , HA [auth F] , KA [auth G] , L [auth A] , N [auth B] , P [auth B] , 
BA [auth E], DA [auth F], FA [auth F], HA [auth F], KA [auth G], L [auth A], N [auth B], P [auth B], R [auth B], RA [auth J], T [auth C], V [auth D], X [auth D], Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SRO PDBBind:  2YMD Kd: 6.93e+5 (nM) from 1 assay(s)
Binding MOAD:  2YMD Kd: 6.93e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.565α = 90
b = 140.064β = 99.08
c = 126.528γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references