1UW6

X-ray structure of acetylcholine binding protein (AChBP) in complex with nicotine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nicotine and Carbamylcholine Binding to Nicotinic Acetylcholine Receptors as Studied in Achbp Crystal Structures

Celie, P.H.N.Van Rossum-Fikkert, S.E.Van Dijk, W.J.Brejc, K.Smit, A.B.Sixma, T.K.

(2004) Neuron 41: 907

  • DOI: 10.1016/s0896-6273(04)00115-1
  • Primary Citation of Related Structures:  
    1UV6, 1UX2, 1UW6

  • PubMed Abstract: 
  • Nicotinic acetylcholine receptors are prototypes for the pharmaceutically important family of pentameric ligand-gated ion channels. Here we present atomic resolution structures of nicotine and carbamylcholine binding to AChBP, a water-soluble homolog of the ligand binding domain of nicotinic receptors and their family members, GABAA, GABAC, 5HT3 serotonin, and glycine receptors ...

    Nicotinic acetylcholine receptors are prototypes for the pharmaceutically important family of pentameric ligand-gated ion channels. Here we present atomic resolution structures of nicotine and carbamylcholine binding to AChBP, a water-soluble homolog of the ligand binding domain of nicotinic receptors and their family members, GABAA, GABAC, 5HT3 serotonin, and glycine receptors. Ligand binding is driven by enthalpy and is accompanied by conformational changes in the ligand binding site. Residues in the binding site contract around the ligand, with the largest movement in the C loop. As expected, the binding is characterized by substantial aromatic and hydrophobic contributions, but additionally there are close contacts between protein oxygens and positively charged groups in the ligands. The higher affinity of nicotine is due to a main chain hydrogen bond with the B loop and a closer packing of the aromatic groups. These structures will be useful tools for the development of new drugs involving nicotinic acetylcholine receptor-associated diseases.


    Related Citations: 
    • Crystal Structure of an Ach-Binding Protein Reveals the Ligand-Binding Domain of Nicotinic Receptors
      Brejc, K., Van Dijk, W.J., Klaassen, R., Schuurmans, M., Van Der Oost, J., Smit, A.B., Sixma, T.K.
      (2001) Nature 411: 269
    • A Glia-Derived Acetylcholine-Binding Protein that Modulates Synaptic Transmission
      Smit, A.B., Syed, N.I., Schaap, D., Van Minnen, J., Klumperman, J., Kits, K.S., Lodder, H., Van Der Schors, R.C., Van Elk, R., Sorgedrager, B., Brejc, K., Sixma, T.K., Geraerts, W.P.M.
      (2001) Nature 411: 261

    Organizational Affiliation

    Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINE-BINDING PROTEIN
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
211Lymnaea stagnalisMutation(s): 0 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCT
Query on NCT

Download Ideal Coordinates CCD File 
AA [auth G] , BA [auth H] , CA [auth I] , DA [auth J] , EA [auth K] , FA [auth L] , GA [auth M] , HA [auth N] , 
AA [auth G],  BA [auth H],  CA [auth I],  DA [auth J],  EA [auth K],  FA [auth L],  GA [auth M],  HA [auth N],  IA [auth O],  JA [auth P],  KA [auth Q],  LA [auth R],  MA [auth S],  NA [auth T],  U [auth A],  V [auth B],  W [auth C],  X [auth D],  Y [auth E],  Z [auth F]
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
C10 H14 N2
SNICXCGAKADSCV-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NCTKd:  479   nM  BindingDB
NCTKi:  100   nM  BindingDB
NCTKi:  331.1300048828125   nM  BindingDB
NCTKi:  83   nM  BindingDB
NCTKd:  316   nM  BindingDB
NCTKd:  320   nM  BindingDB
NCTKd:  310   nM  BindingDB
NCTKd :  45.20000076293945   nM  PDBBind
NCTKd:  45.20000076293945   nM  Binding MOAD
NCTKi:  63.099998474121094   nM  BindingDB
NCTKi:  496   nM  BindingDB
NCTKd:  40.70000076293945   nM  BindingDB
NCTKi:  316.2300109863281   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 233α = 90
b = 267.422β = 90
c = 73.139γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance