2F13

Crystal Structure of the Human Sialidase Neu2 in Complex with 2',3'- dihydroxypropyl ether mimetic Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2F13/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-11-14 Released: 2006-11-21 
• Deposition Author(s): Chavas, L.M.G., Kato, R., Mann, M.C., Thomson, R.J., Dyason, J.C., von Itzstein, M., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.241 
• R-Value Work: 0.194 

Starting Model: experimental

Literature

Crystal Structure of the Human Sialidase Neu2 in Complex with 2',3'- dihydroxypropyl ether mimetic Inhibitor

Chavas, L.M.G., Kato, R., Mann, M.C., Thomson, R.J., Dyason, J.C., von Itzstein, M., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.81 kDa 
• Atom Count: 2,976 
• Modelled Residue Count: 351 
• Deposited Residue Count: 382 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sialidase 2	A	382	Homo sapiens	Mutation(s): 0  EC: 3.2.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3R4 (Homo sapiens) Explore Q9Y3R4  Go to UniProtKB:  Q9Y3R4
PHAROS:  Q9Y3R4 GTEx:  ENSG00000115488

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DYM	C [auth A]	(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid C11 H17 N O8 HEEZEJCEFZJVGN-YRCORFKGSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.241 
• R-Value Work: 0.194 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.5	α = 90
b = 88.06	β = 90
c = 92.59	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Chavas, L.M.G., Kato, R., Mann, M.C., Thomson, R.J., Dyason, J.C., von Itzstein, M., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary