3SAN | pdb_00003san

Crystal structure of influenza A virus neuraminidase N5 complexed with Zanamivir

• PDB DOI: https://doi.org/10.2210/pdb3SAN/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Influenza A virus (A/duck/Alberta/60/1976(H12N5))
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-06-03 Released: 2011-08-10 
• Deposition Author(s): Wang, M.Y., Qi, J.X., Liu, Y., Vavricka, C.J., Wu, Y., Li, Q., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.157 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.120 (Depositor), 0.122 (DCC) 
• R-Value Observed: 
  0.122 (Depositor) 

Starting Model: experimental

Literature

Influenza a virus n5 neuraminidase has an extended 150-cavity

Wang, M.Y., Qi, J.X., Liu, Y., Vavricka, C.J., Wu, Y., Li, Q., Gao, G.F.

(2011) J Virol 85: 8431-8435

• PubMed: 21653672 
• DOI: https://doi.org/10.1128/JVI.00638-11
• Primary Citation Related Structures: 
  3SAL, 3SAN


• PubMed Abstract: 
  

  There are 9 serotypes of neuraminidase (NA) from influenza A virus (N1 to N9), which are classified into two groups based on primary sequences (groups 1 and 2). The structural hallmark of the two groups is the presence or absence of an extra 150-cavity (formed by the 150-loop) in the active site. Thus far, structures of NAs from 6 out of the 9 serotypes have been solved. Here, we solved the N5 structure, the last unknown structure group 1 serotype with a unique Asn147 residue in its 150-loop, demonstrating that it has an extended 150-cavity that closes upon inhibitor binding.

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, The People's Republic of China. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 89.47 kDa 
• Atom Count: 7,380 
• Modeled Residue Count: 788 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B	395	Influenza A virus (A/duck/Alberta/60/1976(H12N5))	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for A1ILL9 (Influenza A virus (strain A/Duck/Alberta/60/1976 H12N5)) Explore A1ILL9  Go to UniProtKB:  A1ILL9
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZMR	G [auth A], L [auth B]	ZANAMIVIR C12 H20 N4 O7 ARAIBEBZBOPLMB-UFGQHTETSA-N
NAG	F [auth A], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	H [auth A], I [auth A], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.157 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.120 (Depositor), 0.122 (DCC) 
• R-Value Observed: 0.122 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.11	α = 90
b = 112.11	β = 90
c = 66.767	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Wang, M.Y., Qi, J.X., Liu, Y., Vavricka, C.J., Wu, Y., Li, Q., Gao, G.F.

Revision History  

• Version 1.0: 2011-08-10
  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: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary