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- PDB-2f10: Crystal Structure of the Human Sialidase Neu2 in Complex with Per... -

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Basic information

Entry
Database: PDB / ID: 2f10
TitleCrystal Structure of the Human Sialidase Neu2 in Complex with Peramivir inhibitor
ComponentsSialidase 2Neuraminidase
KeywordsHYDROLASE / SIALIDASE / NEURAMINIDASE / INFLUENZA VIRUS / PERAMIVIR
Function / homology
Function and homology information


Sialic acid metabolism / glycoprotein catabolic process / glycosphingolipid catabolic process / exo-alpha-sialidase activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity ...Sialic acid metabolism / glycoprotein catabolic process / glycosphingolipid catabolic process / exo-alpha-sialidase activity / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / catalytic complex / lysosome / membrane / cytosol / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-BCZ / PHOSPHATE ION / Sialidase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChavas, L.M.G. / Kato, R. / McKimm-Breschkin, J. / Colman, P.M. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Monti, E. / Wakatsuki, S.
CitationJournal: To be Published
Title: Crystal Structure of the Human Sialidase Neu2 in Complex with Peramivir inhibitor
Authors: Chavas, L.M.G. / Kato, R. / McKimm-Breschkin, J. / Colman, P.M. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Monti, E. / Wakatsuki, S.
History
DepositionNov 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8433
Polymers42,4201
Non-polymers4232
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.340, 92.250, 92.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

Detailsthe monomer in the asymmetric unit forms the biological molecule

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Components

#1: Protein Sialidase 2 / Neuraminidase / Neu2 / Cytosolic sialidase / N-acetyl-alpha- neuraminidase 2


Mass: 42419.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y3R4, exo-alpha-sialidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BCZ / 3-(1-ACETYLAMINO-2-ETHYL-BUTYL)-4-GUANIDINO-2-HYDROXY-CYCLOPENTANECARBOXYLIC ACID / BCX-1812 / Peramivir


Mass: 328.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28N4O4 / Comment: antivirus, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 12, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→63.25 Å / Num. all: 8596 / Num. obs: 8596 / % possible obs: 96.9 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 6.8 / % possible all: 72.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNT

1snt


Resolution: 2.9→46.13 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.292 447 5.2 %RANDOM
Rwork0.215 ---
obs-8149 99.1 %-
Solvent computationBsol: 45.453 Å2
Displacement parametersBiso mean: 43.632 Å2
Baniso -1Baniso -2Baniso -3
1-22.92 Å20 Å20 Å2
2---50.631 Å20 Å2
3---27.711 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 28 25 2801
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.504
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5bcx1812_rep.param

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