5YDI

Crystal structure of acetylcholinesterase catalytic subunits of the malaria vector anopheles gambiae, new crystal packing

• PDB DOI: https://doi.org/10.2210/pdb5YDI/pdb

• Classification: HYDROLASE
• Organism(s): Anopheles gambiae
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-09-13 Released: 2018-03-07 
• Deposition Author(s): Han, Q., Guan, H., Ding, H., Liao, C., Robinson, H., Li, J.
• Funding Organization(s): National Natural Science Foundation of China, NIH

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.242 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 188.42 kDa 
• Atom Count: 12,977 
• Modelled Residue Count: 1,611 
• Deposited Residue Count: 1,659 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B, C	553	Anopheles gambiae	Mutation(s): 0  Gene Names: Ace, ACE1, ACHE1, AGAP001356 EC: 3.1.1.7
UniProt
Find proteins for Q869C3 (Anopheles gambiae) Explore Q869C3  Go to UniProtKB:  Q869C3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G00850LT GlyCosmos:  G00850LT GlyGen:  G00850LT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A], O [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth A], J [auth A], L [auth B], P [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	K [auth A], M [auth B], N [auth B], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.242 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.44	α = 90
b = 235.91	β = 90
c = 167.27	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Han, Q., Guan, H., Ding, H., Liao, C., Robinson, H., Li, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31472186
NIH	United States	AI082581

Revision History  

• Version 1.0: 2018-03-07
  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: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary