1JJB | pdb_00001jjb

A neutral molecule in cation-binding site: Specific binding of PEG-SH to Acetylcholinesterase from Torpedo californica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.224 (Depositor) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1JJB

This is version 1.5 of the entry. See complete history

Literature

A neutral molecule in a cation-binding site: specific binding of a PEG-SH to acetylcholinesterase from Torpedo californica.

Koellner, G.Steiner, T.Millard, C.B.Silman, I.Sussman, J.L.

(2002) J Mol Biology 320: 721-725

  • DOI: https://doi.org/10.1016/s0022-2836(02)00475-8
  • Primary Citation Related Structures: 
    1JJB

  • PubMed Abstract: 

    The crystal structure of acetylcholinesterase from Torpedo californica complexed with the uncharged inhibitor, PEG-SH-350 (containing mainly heptameric polyethylene glycol with a terminal thiol group) is determined at 2.3 A resolution. This is an untypical acetylcholinesterase inhibitor, since it lacks the cationic moiety typical of the substrate (acetylcholine). In the crystal structure, the elongated ligand extends along the whole of the deep and narrow active-site gorge, with the terminal thiol group bound near the bottom, close to the catalytic site. Unexpectedly, the cation-binding site (formed by the faces of aromatic side-chains) is occupied by CH(2) groups of the inhibitor, which are engaged in C-H...pi interactions that structurally mimic the cation-pi interactions made by the choline moiety of acetylcholine. In addition, the PEG-SH molecule makes numerous other weak but specific interactions of the C-H...O and C-H...pi types.


  • Organizational Affiliation
    • Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany. koellner@chemie.fu-berlin.de

Macromolecule Content 

  • Total Structure Weight: 60.98 kDa 
  • Atom Count: 4,874 
  • Modeled Residue Count: 532 
  • Deposited Residue Count: 532 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASE532Tetronarce californicaMutation(s): 0 
EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04058
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE7

Query on PE7



Download:Ideal Coordinates CCD File
D [auth A]1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL
C14 H30 O7 S
ACMBXVJDKVNCGH-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.224 (Depositor) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.2α = 90
b = 111.2β = 90
c = 137.119γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-06-02
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2024-11-20
    Changes: Data collection, Database references, Structure summary