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- PDB-6hg5: Influenza A virus N6 neuraminidase complex with Oseltamivir (Duck... -

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Basic information

Entry
Database: PDB / ID: 6hg5
TitleInfluenza A virus N6 neuraminidase complex with Oseltamivir (Duck/England/56).
ComponentsNeuraminidase
KeywordsHYDROLASE / Influenza / A / Oseltamivir / N6 / Neuraminidase / Duck / Virus / Enzyme / Inhibitor / Complex / GS4071 / Tamiflu
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
CARBON DIOXIDE / Chem-G39 / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSalinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: To Be Published
Title: High Resolution Structures of Viral Neuraminidase with Drugs Bound in the Active Site.
Authors: Salinger, M.T. / Hobbs, J.R. / Murray, J.W. / Laver, W.G. / Kuhn, P. / Garman, E.F.
History
DepositionAug 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Jan 17, 2024Group: 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 13, 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
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,19433
Polymers172,0464
Non-polymers9,14829
Water32,9131827
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29400 Å2
ΔGint35 kcal/mol
Surface area46820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.209, 75.181, 106.386
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Neuraminidase


Mass: 43011.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Duck/England/1/1956 H11N6)
Gene: NA / Production host: Gallus gallus (chicken) / References: UniProt: Q6XV27, exo-alpha-sialidase

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Sugars , 4 types, 11 molecules

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


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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.: 3
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

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Non-polymers , 5 types, 1845 molecules

#6: 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.: 4 / Source method: obtained synthetically / Formula: C14H24N2O4 / Comment: medication*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#9: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CO2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1827 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: N6 crystals were grown by hanging-drop vapour diffusion against 1:1 20%(w/v) PEG-3350 and 2 microM CaCl2 in 150mM NaCl at 20 degrees celsius, starting with equal volumes of N6 (20mg/ml in ...Details: N6 crystals were grown by hanging-drop vapour diffusion against 1:1 20%(w/v) PEG-3350 and 2 microM CaCl2 in 150mM NaCl at 20 degrees celsius, starting with equal volumes of N6 (20mg/ml in saline) and 20% (w/v) PEG 3350 and 2 microM in 1% saline. Microseeding with crystals of native N6 was carried out using a super saturated solution of N6 NA in 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→61.47 Å / Num. obs: 215801 / % possible obs: 98 % / Redundancy: 3.4 % / Rsym value: 0.072 / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5 / Num. unique obs: 10421 / Rsym value: 0.221 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V0Z

1v0z


Resolution: 1.6→61.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.673 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15844 10772 5 %RANDOM
Rwork0.13279 ---
obs0.13408 205029 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.01 Å2
2---0.26 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.6→61.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 605 1827 14468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01413721
X-RAY DIFFRACTIONr_bond_other_d0.0030.01711737
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.70918804
X-RAY DIFFRACTIONr_angle_other_deg1.1371.68627851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg22.0785.571808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83321.731647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.577152112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0811586
X-RAY DIFFRACTIONr_chiral_restr0.110.21941
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217333
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022527
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_it0.4040.5066608
X-RAY DIFFRACTIONr_mcbond_other0.4030.5066607
X-RAY DIFFRACTIONr_mcangle_it0.6570.7598379
X-RAY DIFFRACTIONr_mcangle_other0.6580.7598380
X-RAY DIFFRACTIONr_scbond_it1.0580.6737113
X-RAY DIFFRACTIONr_scbond_other1.0580.6727111
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6310.9710414
X-RAY DIFFRACTIONr_long_range_B_refined5.0218.09116207
X-RAY DIFFRACTIONr_long_range_B_other5.0218.09416208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 766 -
Rwork0.218 14764 -
obs--95.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7565-0.06340.14020.29440.0930.61140.0020.1555-0.0121-0.0257-0.002-0.00780.00240.0465-0.00010.0108-0.00270.00230.04790.00510.005430.5976-1.059551.4104
20.73260.105-0.10950.34020.07220.7836-0.00350.0153-0.0418-0.01960.00090.02530.0654-0.05960.00260.0096-0.0019-0.00170.01140.00330.01181.5579-6.929477.5369
30.8749-0.0907-0.07760.3849-0.1720.61350.0039-0.0048-0.00670.0051-0.0096-0.02320.02090.05860.00570.0056-0.003500.0132-0.00090.001856.9552-1.548380.6836
40.66830.10730.07630.4298-0.11940.6463-0.0012-0.1095-0.04880.0232-0.00230.00890.0123-0.01360.00350.00230.00170.00160.03540.00460.005727.9727-7.2369106.9308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A88 - 512
2X-RAY DIFFRACTION2B88 - 509
3X-RAY DIFFRACTION3C88 - 509
4X-RAY DIFFRACTION4D88 - 509

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