5IH7 | pdb_00005ih7

Acetylcholinesterase of Torpedo californica in complex with the N-methyl-indoxylacetate hydrolysis products

• PDB DOI: https://doi.org/10.2210/pdb5IH7/pdb

• Classification: HYDROLASE
• Organism(s): Tetronarce californica
• Mutation(s): No 


• Deposited: 2016-02-29 Released: 2017-04-05 
• Deposition Author(s): Pesaresi, A., Lamba, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Acetylcholinesterase of Torpedo californica in complex with the N-methyl-indoxylacetate hydrolysis products

Pesaresi, A., Lamba, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.49 kDa 
• Atom Count: 4,635 
• Modelled Residue Count: 534 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A	534	Tetronarce californica	Mutation(s): 0  EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058  Go to UniProtKB:  P04058
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
OMI	D [auth A]	1-methyl-1,2-dihydro-3H-indol-3-one C9 H9 N O DYPFVQQCYZKNMK-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.99	α = 90
b = 111.99	β = 90
c = 137.05	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Pesaresi, A., Lamba, D.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary