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- PDB-2hu4: N1 neuraminidase in complex with oseltamivir 2 -

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Basic information

Entry
Database: PDB / ID: 2hu4
TitleN1 neuraminidase in complex with oseltamivir 2
ComponentsNeuraminidase
KeywordsHYDROLASE / N1 / neuraminidase / oseltamivir
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 / identical protein binding / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-G39 / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,70816
Polymers339,4338
Non-polymers2,2758
Water0
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,8548
Polymers169,7174
Non-polymers1,1374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-63 kcal/mol
Surface area42990 Å2
MethodPISA
2
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,8548
Polymers169,7174
Non-polymers1,1374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-61 kcal/mol
Surface area43140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.060, 201.240, 211.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Neuraminidase / / Neuraminidase NA


Mass: 42429.180 Da / Num. of mol.: 8 / Mutation: H233Y / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / References: UniProt: Q6DPL2
#2: Chemical
ChemComp-G39 / (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid / Oseltamivir carboxylate / Oseltamivir


Mass: 284.351 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication, antivirus*YM

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: MES, PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 147469 / Num. obs: 136759 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.085 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
CrystalClear(MSC/RIGAKU)data collection
AMoREphasing
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 6805 Random
Rwork0.237 --
all0.237 147469 -
obs0.237 136759 -
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23696 0 160 0 23856

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