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- PDB-6br5: N2 neuraminidase in complex with a novel antiviral compound -

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Basic information

Entry
Database: PDB / ID: 6br5
TitleN2 neuraminidase in complex with a novel antiviral compound
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
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-GYG / Neuraminidase / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03790748321 Å
AuthorsLi, L.H. / Ve, T. / Pascolutti, M. / Hadhazi, A. / Bailly, B. / Thomson, R.J. / Gao, G.F. / von Itzstein, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
CitationJournal: ChemMedChem / Year: 2018
Title: A Sulfonozanamivir Analogue Has Potent Anti-influenza Virus Activity.
Authors: Hadhazi, A. / Li, L. / Bailly, B. / Maggioni, A. / Martin, G. / Dirr, L. / Dyason, J.C. / Thomson, R.J. / Gao, G.F. / Borbas, A. / Ve, T. / Pascolutti, M. / von Itzstein, M.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name ..._entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_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

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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)45,0157
Polymers42,7941
Non-polymers2,2216
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,06028
Polymers171,1754
Non-polymers8,88424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area23750 Å2
ΔGint17 kcal/mol
Surface area47030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.056, 110.056, 70.081
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 42793.816 Da / Num. of mol.: 1 / Fragment: Head of neuraminidase domain, residues 83-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: C6KNH8, UniProt: E0UY46*PLUS, exo-alpha-sialidase

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Sugars , 4 types, 4 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.: 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
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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 / N-Acetylglucosamine


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
#7: Sugar ChemComp-GYG / (1R)-4-acetamido-1,5-anhydro-3-carbamimidamido-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol / (1R)-4-(acetylamino)-1,5-anhydro-3-carbamimidamido-2,3,4-trideoxy-1-sulfo-D-glycero-D-galacto-octitol


Type: D-saccharide / Mass: 370.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H22N4O8S

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Non-polymers , 3 types, 195 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.1M Tris, pH 8.0 20% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→43.28 Å / Num. obs: 28004 / % possible obs: 99.6 % / Redundancy: 14.4 % / Biso Wilson estimate: 28.8657008157 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.029 / Rrim(I) all: 0.11 / Net I/σ(I): 20.1
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1919 / CC1/2: 0.933 / Rpim(I) all: 0.253 / Rrim(I) all: 0.953 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gzo

4gzo


Resolution: 2.03790748321→38.9106719551 Å / SU ML: 0.241126432035 / Cross valid method: FREE R-VALUE / σ(F): 1.33627498404 / Phase error: 27.4972843097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221634987539 1403 5.02165431834 %
Rwork0.166038958628 26536 -
obs0.168872122738 27939 99.5084944973 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9055592389 Å2
Refinement stepCycle: LAST / Resolution: 2.03790748321→38.9106719551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 145 193 3335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007244418593753225
X-RAY DIFFRACTIONf_angle_d0.9495020926374395
X-RAY DIFFRACTIONf_chiral_restr0.0584585003856501
X-RAY DIFFRACTIONf_plane_restr0.00583825109265550
X-RAY DIFFRACTIONf_dihedral_angle_d10.59806511381906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0379-2.11070.3117367075551140.2637532150952544X-RAY DIFFRACTION96.3392533527
2.1107-2.19520.2927434615061320.2274024925552615X-RAY DIFFRACTION99.782055939
2.1952-2.29510.297045993471410.2079766924562601X-RAY DIFFRACTION99.8543335761
2.2951-2.41610.2846285499691300.2061080069872645X-RAY DIFFRACTION99.8201438849
2.4161-2.56750.2583443670551490.1890041806322606X-RAY DIFFRACTION99.8912255257
2.5675-2.76570.2384140200681470.1868201563112638X-RAY DIFFRACTION99.9641062455
2.7657-3.04390.2446948588511350.1814904109452676X-RAY DIFFRACTION99.8224431818
3.0439-3.48410.2199594445361460.1601045255442656X-RAY DIFFRACTION99.857448325
3.4841-4.38860.1877920262381440.1305209691992711X-RAY DIFFRACTION99.8600909409
4.3886-38.91770.1744824128941650.1372840280882844X-RAY DIFFRACTION99.8341074983
Refinement TLS params.Method: refined / Origin x: 2.53724259314 Å / Origin y: 27.4877424156 Å / Origin z: 18.3875030407 Å
111213212223313233
T0.261356167822 Å20.0143004633355 Å2-0.0276408365571 Å2-0.200099189067 Å2-0.0411621910301 Å2--0.384129296066 Å2
L1.17640110484 °2-0.122319054393 °20.0266834135784 °2-1.25914383734 °2-0.156679593339 °2--0.538243759131 °2
S0.000311264506009 Å °0.0898225191934 Å °-0.4324930577 Å °-0.102964828116 Å °0.0306489412847 Å °0.0391956171652 Å °0.204096700469 Å °0.0107082940316 Å °-0.0298960666386 Å °
Refinement TLS groupSelection details: all

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