4ARA

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

PDB DOI: https://doi.org/10.2210/pdb4ARA/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2012-04-23 Released: 2012-11-28
Deposition Author(s): Berg, L., Niemiec, M.S., Qian, W., Andersson, C.D., WittungStafshede, P., Ekstrom, F., Linusson, A.

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.4 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

PubMed: 23161758 Search on PubMed
DOI: https://doi.org/10.1002/anie.201205113
Primary Citation of Related Structures:
4ARA, 4ARB

Organizational Affiliation

Department of Chemistry, Umeå University, 90187 Umeå, Sweden.

Macromolecule Content

Total Structure Weight: 123.56 kDa
Atom Count: 9,217
Modelled Residue Count: 1,068
Deposited Residue Count: 1,096
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINESTERASE	A, B	548	Mus musculus	Mutation(s): 0 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21836
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P21836-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C56 Query on C56 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	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		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B]	I [auth A], M [auth A], V [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth A] Focus chain V [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B]	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		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain W [auth B] SDF format, chain Z [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B]	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		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain W [auth B] Focus chain Z [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain W [auth B] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
C56	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 = 78.764	α = 90
b = 112.012	β = 90
c = 227.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-28

Deposition Author(s):

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
Version 2.3: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.4: 2024-11-20
Changes: Structure summary