Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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: 88.09 kDa 
• Atom Count: 6641 
• Modelled Residue Count: 780 
• Deposited Residue Count: 780 
• Unique protein chains: 1

1A4G

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

• PDB DOI: 10.2210/pdb1A4G/pdb

• Classification: HYDROLASE
• Organism(s): Influenza B virus (STRAIN B/BEIJING/1/87)
• Mutation(s): No 


• 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: 2.20 Å
• R-Value Work: 0.198 
• R-Value Observed: 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:  
  1A4G, 1A4Q, 1BJI


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEURAMINIDASE	A, B	390	Influenza B virus (STRAIN B/BEIJING/1/87)	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for P27907 (Influenza B virus (strain B/Beijing/1/1987)) Explore P27907  Go to UniProtKB:  P27907

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZMR	E [auth A], I [auth B]	ZANAMIVIR C12 H20 N4 O7 ARAIBEBZBOPLMB-UFGQHTETSA-N
NAG	C [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	D [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZMR	Binding MOAD:  1A4G	IC50: 4 (nM) from 1 assay(s)
	PDBBind:  1A4G	IC50: 4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.2	α = 90
b = 88.2	β = 90
c = 221.1	γ = 120

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary