4CPZ

Structure of the Neuraminidase from the B/Lyon/CHU/15.216/2011 virus in complex with Zanamivir


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

A Novel I221 L Substitution in Neuraminidase Confers High Level Resistance to Oseltamivir in Influenza B Viruses.

Escuret, V.Collins, P.J.Casalegno, J.Vachieri, S.G.Cattle, N.Ferraris, O.Sabatier, M.Frobert, E.Caro, V.Skehel, J.J.Gamblin, S.Valla, F.Valette, M.Ottmann, M.Mccauley, J.W.Daniels, R.S.Lina, B.

(2014) J Infect Dis 210: 1260

  • DOI: 10.1093/infdis/jiu244
  • Primary Citation of Related Structures:  
    4CPY, 4CPZ, 4CPL, 4CPM, 4CPN, 4CPO

  • PubMed Abstract: 
  • Influenza B viruses with a novel I221L substitution in neuraminidase (NA) conferring high-level resistance to oseltamivir were isolated from an immunocompromised patient after prolonged oseltamivir treatment.


    Organizational Affiliation

    Laboratoire de Virologie et Centre National de Référence virus influenzae Laboratoire Virpath EA4610, Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Université de Lyon, and.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEURAMINIDASEA, B, C, D, E, F, G, H466Influenza B virusMutation(s): 0 
EC: 3.2.1.18
UniProt
Find proteins for U5XBU0 (Influenza B virus)
Explore U5XBU0 
Go to UniProtKB:  U5XBU0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI, J, L, M, N, O3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK, P2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZMR (Subject of Investigation/LOI)
Query on ZMR

Download Ideal Coordinates CCD File 
BA [auth D], FA [auth E], HA [auth F], KA [auth G], NA [auth H], S [auth A], V [auth B], Y [auth C]ZANAMIVIR
C12 H20 N4 O7
ARAIBEBZBOPLMB-UFGQHTETSA-N
 Ligand Interaction
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D], EA [auth E], JA [auth G], MA [auth H], R [auth A], U [auth B], X [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
DA [auth E], GA [auth F], IA [auth G], LA [auth H], Q [auth A], T [auth B], W [auth C], Z [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZMR Binding MOAD:  4CPZ Ki: 20.85 (nM) from 1 assay(s)
BindingDB:  4CPZ Ki: 0.1 (nM) from 1 assay(s)
IC50: min: 1.7, max: 434 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.344α = 90
b = 163.255β = 108.31
c = 123.451γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2015-04-01
    Changes: Derived calculations
  • Version 1.3: 2019-10-02
    Changes: Data collection, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary