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Basic information

Entry
Database: PDB / ID: 5jyy
TitleStructure-based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-resistant Influenza Viruses
ComponentsNeuraminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / neuraminidase inhibitor / tetravalent Zanamivir / 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-6PY / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFu, L. / Wu, Y. / Bi, Y. / Zhang, S. / Lv, X. / Qi, J. / Li, Y. / Lu, X. / Yan, J. / Gao, G.F. / Li, X.
Funding support China, 3items
OrganizationGrant numberCountry
the Ministry of Science and Technology of China2012CB518803 China
National Natural Science Foundation of China31470801, 81273381, 21202195, 81301465 and 81330082 China
Youth Innovation Promotion Association, CAS2016086 China
Citation
Journal: J.Med.Chem. / Year: 2016
Title: Structure-Based Tetravalent Zanamivir with Potent Inhibitory Activity against Drug-Resistant Influenza Viruses
Authors: Fu, L. / Bi, Y. / Wu, Y. / Zhang, S. / Qi, J. / Li, Y. / Lu, X. / Zhang, Z. / Lv, X. / Yan, J. / Gao, G.F. / Li, X.
#1: Journal: Cell Res. / Year: 2013
Title: Characterization of two distinct neuraminidases from avian-origin human-infecting H7N9 influenza viruses
Authors: Wu, Y. / Bi, Y. / Vavricka, C.J. / Sun, X. / Zhang, Y. / Gao, F. / Zhao, M. / Xiao, H. / Qin, C. / He, J. / Liu, W. / Yan, J. / Qi, J. / Gao, G.F.
History
DepositionMay 15, 2016Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 29, 2016ID: 5E6L
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Aug 16, 2017Group: Database references / Derived calculations
Category: citation / pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type
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.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.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 / _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 2.1Nov 8, 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)46,0016
Polymers43,5261
Non-polymers2,4755
Water6,738374
1
A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules

A: Neuraminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,00324
Polymers174,1024
Non-polymers9,90120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_975-x+4,-y+2,z1
crystal symmetry operation15_685y+1,-x+3,z1
crystal symmetry operation16_845-y+3,x-1,z1
Buried area26040 Å2
ΔGint89 kcal/mol
Surface area46060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.079, 180.079, 180.079
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-872-

HOH

21A-930-

HOH

31A-964-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neuraminidase /


Mass: 43525.500 Da / Num. of mol.: 1 / Fragment: UNP residues 78-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/01/2013(H7N9) / Gene: NA / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: R4NFR6, exo-alpha-sialidase

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Sugars , 3 types, 4 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: 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.: 2
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
#5: Sugar ChemComp-6PY / 5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-enon ic acid / 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2- enonic acid


Type: D-saccharide / Mass: 433.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N5O9

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Non-polymers , 2 types, 375 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThis conflict is due to difference of strain.

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 5%(v/v) 2-methyl-2,4-pentanediol, 10%(v/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29294 / % possible obs: 100 % / Redundancy: 12 % / Net I/σ(I): 21.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 3.54 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NN9

7nn9


Resolution: 2.1→35.316 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.06
RfactorNum. reflection% reflection
Rfree0.1715 1483 5.06 %
Rwork0.1507 --
obs0.1518 29288 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→35.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 164 374 3591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063349
X-RAY DIFFRACTIONf_angle_d1.0344572
X-RAY DIFFRACTIONf_dihedral_angle_d11.9561240
X-RAY DIFFRACTIONf_chiral_restr0.045514
X-RAY DIFFRACTIONf_plane_restr0.004577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.16770.23651190.1852507X-RAY DIFFRACTION100
2.1677-2.24510.20571470.17682472X-RAY DIFFRACTION100
2.2451-2.3350.22461140.16622493X-RAY DIFFRACTION100
2.335-2.44130.20161360.1742499X-RAY DIFFRACTION100
2.4413-2.56990.21061380.17222494X-RAY DIFFRACTION100
2.5699-2.73090.20891220.17172497X-RAY DIFFRACTION100
2.7309-2.94170.1841640.16782485X-RAY DIFFRACTION100
2.9417-3.23750.18821220.15762531X-RAY DIFFRACTION100
3.2375-3.70550.16041380.14212540X-RAY DIFFRACTION100
3.7055-4.66690.13011500.11562565X-RAY DIFFRACTION100
4.6669-35.32140.15221330.14542722X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 379.9239 Å / Origin y: 160.3875 Å / Origin z: 54.559 Å
111213212223313233
T0.2369 Å20.0104 Å20.002 Å2-0.2435 Å2-0.0156 Å2--0.2135 Å2
L0.5872 °2-0.0239 °2-0.0361 °2-0.4256 °20.0045 °2--0.1987 °2
S0.0055 Å °0.0612 Å °-0.0794 Å °-0.0371 Å °0.0105 Å °-0.0684 Å °0.0301 Å °0.0367 Å °-0.016 Å °
Refinement TLS groupSelection details: all

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