1UW6

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 

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

  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINE-BINDING PROTEIN
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
211Lymnaea stagnalisMutation(s): 0 
Find proteins for P58154 (Lymnaea stagnalis)
Go to UniProtKB:  P58154
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCT
Query on NCT
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
(S)-(-)-NICOTINE, 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE
C10 H14 N2
SNICXCGAKADSCV-JTQLQIEISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NCTKd: 40.7 - 479 nM (99) BINDINGDB
NCTKi: 63.1 - 496 nM (99) BINDINGDB
NCTKd: 45.2 nM BINDINGMOAD
NCTKd: 45.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 233.000α = 90.00
b = 267.422β = 90.00
c = 73.139γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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