2Y2V | pdb_00002y2v

Nonaged form of Mouse Acetylcholinesterase inhibited by sarin-Update

PDB DOI: https://doi.org/10.2210/pdb2Y2V/pdb
Entry: 2Y2V supersedes: 2JGG

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

Deposited: 2010-12-16 Released: 2011-11-30
Deposition Author(s): Akfur, C., Artursson, E., Ekstrom, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.224 (Depositor), 0.220 (DCC)
R-Value Work:
0.185 (Depositor), 0.182 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Methylphosphonate Adducts of Acetylcholinesterase Investigated by Time Correlated Single Photon Counting and X-Ray Crystallography

Akfur, C., Artursson, E., Ekstrom, F.

To be published.

Macromolecule Content

Total Structure Weight: 122.37 kDa
Atom Count: 9,175
Modeled Residue Count: 1,060
Deposited Residue Count: 1,096
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21836
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P21836-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P15 Query on P15 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL C₁₃ H₂₈ O₇ FHHGCKHKTAJLOM-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B]
ME2 Query on ME2 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE C₇ H₁₆ O₃ CNJRPYFBORAQAU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A]	E [auth A], F [auth A], I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A]
ETX Query on ETX Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-ETHOXYETHANOL C₄ H₁₀ O₂ ZNQVEEAIQZEUHB-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SGB Query on SGB	A, B	L-PEPTIDE LINKING	C₇ H₁₆ N O₅ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.224 (Depositor), 0.220 (DCC)
R-Value Work: 0.185 (Depositor), 0.182 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.488	α = 90
b = 111.643	β = 90
c = 227.026	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-11-30

Deposition Author(s):

Akfur, C.

Artursson, E.

Ekstrom, F.

This entry supersedes: 2JGG

Revision History (Full details and data files)

Version 1.0: 2011-11-30
Type: Initial release
Version 1.1: 2013-05-01
Changes: Other
Version 1.2: 2018-01-17
Changes: Advisory, Data collection
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-20
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary

2Y2V | pdb_00002y2v

Nonaged form of Mouse Acetylcholinesterase inhibited by sarin-Update

Literature

Methylphosphonate Adducts of Acetylcholinesterase Investigated by Time Correlated Single Photon Counting and X-Ray Crystallography

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

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