Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 88085.78 
• Atom Count: 6149 
• Residue Count: 780 
• Unique protein chains: 1

1A4G

INFLUENZA VIRUS B/BEIJING/1/87 NEURAMINIDASE COMPLEXED WITH ZANAMIVIR

• DOI: 10.2210/pdb1A4G/pdb

• Classification: HYDROLASE
• Organism(s): Influenza B virus (strain B/Beijing/1/1987)


• Deposited: 1998-01-29 Released: 1999-03-02 
• Deposition Author(s): Cleasby, A., Singh, O., Skarzynski, T., Wonacott, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.198 

Literature

Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B.

Taylor, N.R., Cleasby, A., Singh, O., Skarzynski, T., Wonacott, A.J., Smith, P.W., Sollis, S.L., Howes, P.D., Cherry, P.C., Bethell, R., Colman, P., Varghese, J.

(1998) J.Med.Chem. 41: 798-807

• PubMed: 9526556 
• DOI: 10.1021/jm9703754
• Primary Citation of Related Structures:  
  1BJI, 1A4Q


• PubMed Abstract: 
  

The first paper in this series (see previous article) described structure-activity studies of carboxamide analogues of zanamivir binding to influenza virus sialidase types A and B and showed that inhibitory activity of these compounds was much greater against influenza A enzyme. To understand the large differences in affinities, a number of protein-ligand complexes have been investigated using crystallography and molecular dynamics. The crystallographic studies show that the binding of ligands containing tertiary amide groups is accompanied by the formation of an intramolecular planar salt bridge between two amino acid residues in the active site of the enzyme. It is proposed that the unexpected strong binding of these inhibitors is a result of the burial of hydrophobic surface area and salt-bridge formation in an environment of low dielectric. In sialidase from type A virus, binding of the carboxamide moeity and salt-bridge formation have only a minor effect on the positions of the surrounding residues, whereas in type B enzyme, significant distortion of the protein is observed. The results suggest that the decreased affinity in enzyme from influenza B is directly correlated with the small changes that occur in the amino acid residue interactions accompanying ligand binding. Molecular dynamics calculations have shown that the tendency for salt-bridge formation is greater in influenza A sialidase than influenza B sialidase and that this tendency is a useful descriptor for the prediction of inhibitor potency.

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Related Citations: 

• The 2.2 A Resolution Crystal Structure of Influenza B Neuraminidase and its Complex with Sialic Acid
  Burmeister, W.P.,Ruigrok, R.W.,Cusack, S.
  (1992) Embo J. 11: 49
• Sequence and Crystallization of Influenza Virus B/Beijing/1/87 Neuraminidase
  Burmeister, W.P.,Daniels, R.S.,Dayan, S.,Gagnon, J.,Cusack, S.,Ruigrok, R.W.
  (1991) Virology 180: 266




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Organizational Affiliation: 

Department of Biomolecular Structure, Glaxo Wellcome Research and Development Limited, Hertfordshire, U.K.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NEURAMINIDASE	A, B	390	Influenza B virus (strain B/Beijing/1/1987)	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
Find proteins for P27907 (Influenza B virus (strain B/Beijing/1/1987)) Go to UniProtKB:  P27907

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
ZMR	A, B	ZANAMIVIR MODIFIED SIALIC ACID C12 H20 N4 O7 ARAIBEBZBOPLMB-UFGQHTETSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZMR	Ki: 0.1 nM (94) BINDINGDB
ZMR	IC50: 1.7 - 20 nM (94) BINDINGDB
ZMR	IC50: 4 nM BINDINGMOAD
ZMR	IC50: 4 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Work: 0.198 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 88.200	α = 90.00
b = 88.200	β = 90.00
c = 221.100	γ = 120.00

Software Package:

Software Name	Purpose
CCP4	data scaling
CCP4	data reduction
X-PLOR	refinement
X-PLOR	model building
X-PLOR	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-01-29 
• Released Date: 1999-03-02 
• Deposition Author(s): Cleasby, A., Singh, O., Skarzynski, T., Wonacott, A.J.

Revision History 

• Version 1.0: 1999-03-02
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance