5HF9

Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6

PDB DOI: https://doi.org/10.2210/pdb5HF9/pdb

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

Deposited: 2016-01-06 Released: 2016-06-22
Deposition Author(s): Franklin, M.F., Rudolph, M.J., Ginter, C., Cassidy, M.S., Cheung, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240
R-Value Work: 0.201
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 121.79 kDa
Atom Count: 9,133
Modelled Residue Count: 1,063
Deposited Residue Count: 1,084
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22303
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
HI6 Query on HI6 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B]	H [auth A], O [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 H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
DEP Query on DEP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B]	E [auth A], J [auth B]	DIETHYL PHOSPHONATE C₄ H₁₁ O₃ P MJUJXFBTEFXVKU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	F [auth A], G [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
HI6	BindingDB: 5HF9	Kd: min: 1.50e+4, max: 2.34e+5 (nM) from 6 assay(s)
HI6	BindingDB: 5HF9	IC50: min: 6.36e+5, max: 1.36e+6 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.240
R-Value Work: 0.201
R-Value Observed: 0.203
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.931	α = 90
b = 105.931	β = 90
c = 324.415	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2016-08-24
Changes: Database references
Version 1.2: 2017-11-22
Changes: Database references, Derived calculations, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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Help and Resources

5HF9

Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)