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- PDB-2htq: N8 neuraminidase in complex with zanamivir -

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Basic information

Entry
Database: PDB / ID: 2htq
TitleN8 neuraminidase in complex with zanamivir
ComponentsNeuraminidase
KeywordsHYDROLASE / N8 / neuraminidase / zanamivir
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
ZANAMIVIR / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRussell, R.J. / Haire, L.F. / Stevens, D.J. / Collins, P.J. / Lin, Y.P. / Blackburn, G.M. / Hay, A.J. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Nature / Year: 2006
Title: The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.
Authors: Russell, R.J. / Haire, L.F. / Stevens, D.J. / Collins, P.J. / Lin, Y.P. / Blackburn, G.M. / Hay, A.J. / Gamblin, S.J. / Skehel, J.J.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4902
Polymers43,1581
Non-polymers3321
Water1,856103
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9598
Polymers172,6304
Non-polymers1,3294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.400, 90.400, 109.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Neuraminidase /


Mass: 43157.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / References: UniProt: Q07599, exo-alpha-sialidase
#2: Sugar ChemComp-ZMR / ZANAMIVIR / MODIFIED SIALIC ACID / Zanamivir


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Imidazole, MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 22271 / Num. obs: 20267 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.079 / Net I/σ(I): 9.9
Reflection shellResolution: 2.2→2.3 Å / % possible all: 54.6

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.334 709 Random
Rwork0.271 --
obs0.271 20267 -
all-22271 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 23 103 3124

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