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- PDB-2hu0: N1 neuraminidase in complex with oseltamivir 1 -

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Basic information

Entry
Database: PDB / ID: 2hu0
TitleN1 neuraminidase in complex with oseltamivir 1
ComponentsNeuraminidase
KeywordsHYDROLASE / N1 / neuraminidase / oseltamivir
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 / identical protein binding / membrane
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: 2.95 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)339,7189
Polymers339,4338
Non-polymers2841
Water00
1
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,0015
Polymers169,7174
Non-polymers2841
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-57 kcal/mol
Surface area43070 Å2
MethodPISA
2
E: Neuraminidase
F: Neuraminidase
G: Neuraminidase
H: Neuraminidase


Theoretical massNumber of molelcules
Total (without water)169,7174
Polymers169,7174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-58 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.083, 200.576, 210.417
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: H253Y / 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


Mass: 284.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication*YM
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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MES, PEG3350, 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 / 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: 2.95→30 Å / Num. all: 88347 / Num. obs: 70678 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→142.86 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.793 / SU B: 18.895 / SU ML: 0.356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 3705 5 %RANDOM
Rwork0.21754 ---
obs0.22136 70636 79.11 %-
all-88347 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.95→142.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23696 0 20 0 23716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02224052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2831.92232643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.74352968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21923.8641056
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.311153671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7415128
X-RAY DIFFRACTIONr_chiral_restr0.1560.23428
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218468
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.210794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.215505
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2836
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3690.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.515477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.459224072
X-RAY DIFFRACTIONr_scbond_it2.073310398
X-RAY DIFFRACTIONr_scangle_it3.3074.58571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.95 Å / Num. reflection Rwork: 4782 / Total num. of bins used: 20

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