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- PDB-2htw: N4 neuraminidase in complex with DANA -

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Basic information

Entry
Database: PDB / ID: 2htw
TitleN4 neuraminidase in complex with DANA
ComponentsNeuraminidase
KeywordsHYDROLASE / N4 / neuraminidase / DANA
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 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: 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
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2242
Polymers42,9331
Non-polymers2911
Water00
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8978
Polymers171,7324
Non-polymers1,1654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area14280 Å2
ΔGint-54 kcal/mol
Surface area44110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)193.400, 193.400, 193.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Neuraminidase


Mass: 42932.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / References: UniProt: Q6XV46
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17NO8
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, PEG3350, pH 7.5, 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: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 8112 / Num. obs: 7998 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 378 Random
Rwork0.217 --
obs0.217 7998 -
all-8112 -
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 20 0 3015

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