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- PDB-1nnc: INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) COMPLEXED WITH 4-... -

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Entry
Database: PDB / ID: 1nnc
TitleINFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) COMPLEXED WITH 4-GUANIDINO-NEU5AC2EN INHIBITOR
ComponentsNEURAMINIDASE N9
KeywordsHYDROLASE (O-GLUCOSYL) / NEURAMINIDASE / SIALIDASE
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
alpha-D-mannopyranose / ZANAMIVIR / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsVarghese, J.N. / Colman, P.M.
Citation
Journal: Protein Sci. / Year: 1995
Title: Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase.
Authors: Varghese, J.N. / Epa, V.C. / Colman, P.M.
#1: Journal: Nature / Year: 1993
Title: Rational Design of Potent Sialidase-Based Inhibitors of Influenza Virus Replication
Authors: Von Itzstein, M. / Wu, W.-Y. / Kok, G.B. / Pegg, M.S. / Dyason, J.C. / Jin, B. / Van Phan, T. / Smythe, M.L. / White, H.F. / Oliver, S.W. / Colman, P.M. / Varghese, J.N. / Ryan, D.M. / ...Authors: Von Itzstein, M. / Wu, W.-Y. / Kok, G.B. / Pegg, M.S. / Dyason, J.C. / Jin, B. / Van Phan, T. / Smythe, M.L. / White, H.F. / Oliver, S.W. / Colman, P.M. / Varghese, J.N. / Ryan, D.M. / Woods, J.M. / Bethell, R.C. / Hotham, V.J. / Cameron, J.M. / Penn, C.R.
#2: Journal: Proteins / Year: 1992
Title: The Structure of the Complex between Influenza Virus Neuraminidase and Sialic Acid, the Viral Receptor
Authors: Varghese, J.N. / Mckimm-Breschkin, J.L. / Caldwell, J.B. / Kortt, A.A. / Colman, P.M.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Atomic Structures of N9 Subtype Influenza Virus Neuraminidase and Escape Mutants
Authors: Tulip, W.R. / Varghese, J.N. / Baker, A.T. / Van Donkelaar, A. / Laver, W.G. / Webster, R.G. / Colman, P.M.
#4: Journal: J.Mol.Biol. / Year: 1991
Title: Three-Dimensional Structure of the Neuraminidase of Influenza Virus A(Slash)Tokyo(Slash)3(Slash)67 at 2.2 Angstroms Resolution
Authors: Varghese, J.N. / Colman, P.M.
#5: Journal: Proteins / Year: 1987
Title: The Three-Dimensional Structure of Neuraminidase of Subtype N9 from an Avian Influenza Virus
Authors: Baker, A.T. / Varghese, J.N. / Laver, W.G. / Air, G.M. / Colman, P.M.
#6: Journal: Nature / Year: 1983
Title: Structure of the Influenza Virus Glycoprotein Antigen Neuraminidase at 2.9 Angstroms Resolution
Authors: Varghese, J.N. / Laver, W.G. / Colman, P.M.
History
DepositionMar 15, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_PDB_ins_code / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAMINIDASE N9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7927
Polymers43,7241
Non-polymers2,0686
Water3,549197
1
A: NEURAMINIDASE N9
hetero molecules

A: NEURAMINIDASE N9
hetero molecules

A: NEURAMINIDASE N9
hetero molecules

A: NEURAMINIDASE N9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,16728
Polymers174,8954
Non-polymers8,27224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)182.800, 182.800, 182.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Atom site foot note1: CIS PROLINE - PRO 326 / 2: CIS PROLINE - PRO 431
Components on special symmetry positions
IDModelComponents
11A-664-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NEURAMINIDASE N9 / SIALIDASE / HYDROLASE (O-GLYCOSYL)


Mass: 43723.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/TERN/AUSTRALIA/G70C/75 / References: UniProt: P03472, exo-alpha-sialidase

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Sugars , 4 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_d2-e1_e2-f1WURCSPDB2Glycan 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]{}}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#6: Sugar ChemComp-ZMR / ZANAMIVIR / MODIFIED SIALIC ACID / Zanamivir


Type: D-saccharide / Mass: 332.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O7 / Comment: medication, inhibitor*YM

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Non-polymers , 2 types, 198 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Source detailsMOLECULE_NAME: N9 NEURAMINIDASE. GROWN IN CHICK EMBRYO

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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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
21.7 Mpotassium phosphate1drop
31.9 Mpotassium phosphate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNum. obs: 29729 / % possible obs: 63 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 106232 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.8 Å / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
WEISMERGING R-FACTOR (INTENSITY) : 0.09data collection
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
X-PLORphasing
RefinementResolution: 1.8→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.156 -
obs0.156 28364
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 135 197 3399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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