4ARA

Mus musculus Acetylcholinesterase in complex with (R)-C5685 at 2.5 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Similar But Different: Thermodynamic and Structural Characterization of a Pair of Enantiomers Binding to Acetylcholinesterase.

Berg, L.Niemiec, M.S.Qian, W.Andersson, C.D.Wittung-Stafshede, P.Ekstrom, F.Linusson, A.

(2012) Angew Chem Int Ed Engl 51: 12716


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASEA, B548Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus)
Explore P21836 
Go to UniProtKB:  P21836
IMPC:  MGI:87876
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21836
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C56
Query on C56

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
4-(DIMETHYLAMINO)-N-{[(2R)-1-ETHYLPYRROLIDIN-2-YL]METHYL}-2-METHOXY-5-NITROBENZAMIDE
C17 H26 N4 O4
AFNPLUMDSLEAPD-GFCCVEGCSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
P [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
M [auth A],
V [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A],
O [auth B],
Q [auth B],
D [auth A],
F [auth A],
G [auth A],
O [auth B],
Q [auth B],
R [auth B],
T [auth B],
U [auth B],
X [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
E [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
S [auth B],
W [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
Y [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C56 Binding MOAD:  4ARA Kd: 900 (nM) from 1 assay(s)
PDBBind:  4ARA Kd: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.764α = 90
b = 112.012β = 90
c = 227.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references
  • Version 2.0: 2018-01-17
    Changes: Atomic model, Data collection
  • Version 2.1: 2018-02-28
    Changes: Source and taxonomy
  • Version 2.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary