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- PDB-5w2y: INFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 9-DEOXYGENATED 2... -

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Basic information

Entry
Database: PDB / ID: 5w2y
TitleINFLUENZA VIRUS NEURAMINIDASE N9 IN COMPLEX WITH 9-DEOXYGENATED 2,3-DIFLUORO-N-ACETYLNEURAMINIC ACID
ComponentsNeuraminidase
Keywordshydrolase/hydrolase inhibitor / INFLUENZA VIRUS NEURAMINIDASE / N9 / COMPLEX / 2 / 3-DIFLUOROSIALIC ACID / SECOND BINDING SITE / HYDROLASE / hydrolase-hydrolase inhibitor complex
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
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Chem-9T1 / Chem-9T7 / Chem-9TM / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsStreltsov, V.A. / Mckimm-Breschkin, J. / Barrett, S. / Pilling, P. / Hader, S. / Watt, A.G.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structural and Functional Analysis of Anti-Influenza Activity of 4-, 7-, 8- and 9-Deoxygenated 2,3-Difluoro- N-acetylneuraminic Acid Derivatives.
Authors: McKimm-Breschkin, J.L. / Barrett, S. / Pilling, P.A. / Hader, S. / Watts, A.G. / Streltsov, V.A.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8708
Polymers43,7241
Non-polymers3,1467
Water6,341352
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,47832
Polymers174,8954
Non-polymers12,58328
Water724
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 area26820 Å2
ΔGint101 kcal/mol
Surface area47660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.383, 181.383, 181.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-807-

HOH

21A-946-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase


Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 82-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)
Strain: A/Tern/Australia/G70C/1975 H11N9 / Gene: NA / Cell line (production host): HIGH FIVE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03472, exo-alpha-sialidase

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Sugars , 5 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-9T7 / (2R,3R,4R,5R,6R)-5-acetamido-6-[(1R,2R)-1,2-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxane-2-carboxylic acid / (2~{R},3~{R},4~{R},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-1,2-bis(oxidanyl)propyl]-2,3-bis(fluoranyl)-4-oxidanyl-oxa ne-2-carboxylic acid


Type: D-saccharide / Mass: 313.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17F2NO7
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-9T1 / 5-acetamido-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid / 5-(acetylamino)-2,6-anhydro-3,5,9-trideoxy-3-fluoro-D-erythro-L-gluco-non-4-ulosonic acid


Type: L-saccharide / Mass: 293.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16FNO7

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Non-polymers , 3 types, 354 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-9TM / (2~{R},3~{R},4~{R},5~{R})-3-acetamido-2-[(1~{R},2~{R})-1,2-bis(oxidanyl)propyl]-5-fluoranyl-4-oxidanyl-2,3,4,5-tetrahydropyran-1-ium-6-carboxylic acid


Mass: 294.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17FNO7
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 1.7M POTASSIUM PHOSPHATE / PH range: 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953733 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953733 Å / Relative weight: 1
ReflectionResolution: 2.39→48.48 Å / Num. obs: 19147 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 35.4 % / Rmerge(I) obs: 0.394 / Net I/σ(I): 11.4
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 16.6 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PHASERphasing
XFITmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WEG

4weg


Resolution: 2.39→48.48 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.739 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1035 5.1 %RANDOM
Rwork0.141 ---
obs0.143 19147 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.39→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 209 352 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.023411
X-RAY DIFFRACTIONr_bond_other_d0.0030.023003
X-RAY DIFFRACTIONr_angle_refined_deg1.9372.0014664
X-RAY DIFFRACTIONr_angle_other_deg1.62836970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.6485.103389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93623.311151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50715511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.811527
X-RAY DIFFRACTIONr_chiral_restr0.2050.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213715
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3272.0141554
X-RAY DIFFRACTIONr_mcbond_other1.3132.0131553
X-RAY DIFFRACTIONr_mcangle_it2.083.0171937
X-RAY DIFFRACTIONr_mcangle_other2.0833.0191938
X-RAY DIFFRACTIONr_scbond_it2.772.4811857
X-RAY DIFFRACTIONr_scbond_other2.7712.4811855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4553.632727
X-RAY DIFFRACTIONr_long_range_B_refined8.1541.27215077
X-RAY DIFFRACTIONr_long_range_B_other7.87641.02814787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 85 -
Rwork0.25 1367 -
obs--98.24 %

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