6NTG | pdb_00006ntg

Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-234 in Complex with Reactivator, HI-6

PDB DOI: https://doi.org/10.2210/pdb6NTG/pdb

Classification: HYDROLASE/HYDROLASE Inhibitor
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2019-01-29 Released: 2020-07-01
Deposition Author(s): Bester, S.M., Guelta, M.A., Height, J.J., Pegan, S.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.232 (Depositor), 0.233 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents

Height, J.J., Bester, S.M., Guelta, M.A., Bae, S.Y., Cheung, J., Pegan, S.D.

To be published.

Macromolecule Content

Total Structure Weight: 122.04 kDa
Atom Count: 9,035
Modeled Residue Count: 1,062
Deposited Residue Count: 1,084
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B	542	Homo sapiens	Mutation(s): 0 Gene Names: ACHE EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P22303 (Homo sapiens) Explore P22303 Go to UniProtKB: P22303
PHAROS: P22303 GTEx: ENSG00000087085
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22303
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P22303-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	3		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Interactions & Density Focus chain C Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HI6 Query on HI6 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B]	4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM C₁₄ H₁₆ N₄ O₃ FJZDLOMCEPUCII-UHFFFAOYSA-P		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
L1M Query on L1M Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A], K [auth B]	ethyl (R)-N-[(1E)-1-(diethylamino)ethylidene]phosphonamidate C₈ H₁₉ N₂ O₂ P OJNAFPOCQGTUIK-CMDGGOBGSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
HI6	BindingDB: 6NTG	Kd: min: 1.50e+4, max: 2.34e+5 (nM) from 6 assay(s)
HI6	BindingDB: 6NTG	IC50: min: 6.36e+5, max: 1.36e+6 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.232 (Depositor), 0.233 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.666	α = 90
b = 104.666	β = 90
c = 325.035	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary