7E3D | pdb_00007e3d

Crystal structure of human acetylcholinesterase

PDB DOI: https://doi.org/10.2210/pdb7E3D/pdb

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

Deposited: 2021-02-08 Released: 2022-02-16
Deposition Author(s): Dileep, K.V., Ihara, K., Mishima-Tsumagari, C., Kukimoto-Niino, M., Yonemochi, M., Hanada, K., Shirouzu, M., Zhang, K.Y.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human acetylcholinesterase in complex with tacrine: Implications for drug discovery

Dileep, K., Ihara, K., Mishima-Tsumagari, C., Kukimoto-Niino, M., Yonemochi, M., Hanada, K., Shirouzu, M., Zhang, K.Y.

(2022) Int J Biol Macromol 210: 172-181

DOI: https://doi.org/10.1016/j.ijbiomac.2022.05.009

Macromolecule Content

Total Structure Weight: 119.98 kDa
Atom Count: 8,528
Modeled Residue Count: 1,065
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B	540	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: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P22303-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE8 Query on PE8 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.242 (Depositor), 0.242 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.931	α = 90
b = 104.931	β = 90
c = 322.566	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

Mishima-Tsumagari, C.

Kukimoto-Niino, M.

Revision History (Full details and data files)

Version 1.0: 2022-02-16
Type: Initial release
Version 1.1: 2023-03-01
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.