2BAT

THE STRUCTURE OF THE COMPLEX BETWEEN INFLUENZA VIRUS NEURAMINIDASE AND SIALIC ACID, THE VIRAL RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor.

Varghese, J.N.McKimm-Breschkin, J.L.Caldwell, J.B.Kortt, A.A.Colman, P.M.

(1992) Proteins 14: 327-332

  • DOI: 10.1002/prot.340140302
  • Primary Citation of Related Structures:  
    2BAT

  • PubMed Abstract: 
  • Crystallographic studies of neuraminidase-sialic acid complexes indicate that sialic acid is distorted on binding the enzyme. Three arginine residues on the enzyme interact with the carboxylate group of the sugar which is observed to be equatorial to the saccharide ring as a consequence of its distorted geometry ...

    Crystallographic studies of neuraminidase-sialic acid complexes indicate that sialic acid is distorted on binding the enzyme. Three arginine residues on the enzyme interact with the carboxylate group of the sugar which is observed to be equatorial to the saccharide ring as a consequence of its distorted geometry. The glycosidic oxygen is positioned within hydrogen-bonding distance of Asp-151, implicating this residue in catalysis.


    Related Citations: 
    • Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
      Varghese, J.N., Colman, P.M.
      (1991) J Mol Biol 221: 473
    • Amino Acid Sequence of the Pronase-Released Heads of Neuraminidase Subtype N2 from the Asian Strain A(Slash)Tokyo(Slash)3(Slash)67 of Influenza Virus
      Ward, C.W., Elleman, T.C., Azad, A.A.
      (1982) Biochem J 207: 91

    Organizational Affiliation

    CSIRO, Division of Biomolecular Engineering, Parkville, Victoria, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASE N2A388Influenza A virus (A/Tokyo/3/1967(H2N2))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for P06820 (Influenza A virus (strain A/Tokyo/3/1967 H2N2))
Explore P06820 
Go to UniProtKB:  P06820
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseB7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G29489WX
GlyCosmos:  G29489WX
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseC6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIA (Subject of Investigation/LOI)
Query on SIA

Download Ideal Coordinates CCD File 
F [auth A]N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.6α = 90
b = 139.6β = 90
c = 191γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary