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- PDB-2qwb: THE X-RAY STRUCTURE OF A COMPLEX OF SIALIC ACID AND A DRUG RESIST... -

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Entry
Database: PDB / ID: 2qwb
TitleTHE X-RAY STRUCTURE OF A COMPLEX OF SIALIC ACID AND A DRUG RESISTANT VARIANT R292K OF TERN N9 INFLUENZA VIRUS NEURAMINIDASE
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / NEURAMINIDASE / INFLUENZA PROTEIN / DRUG RESISTANT VARIANT / SIALIC ACID / SECOND BINDING SITE / GLYCOSYLATED PROTEIN
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
N-acetyl-alpha-neuraminic acid / Neuraminidase
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVarghese, J.N.
Citation
Journal: Structure / Year: 1998
Title: Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase.
Authors: Varghese, J.N. / Smith, P.W. / Sollis, S.L. / Blick, T.J. / Sahasrabudhe, A. / McKimm-Breschkin, J.L. / Colman, P.M.
#1: Journal: J.Virol. / Year: 1998
Title: Mutations in a Conserved Residue in the Influenza Virus Neuraminidase Active Site Decreases Sensitivity to Neu5Ac2En-Derived Inhibitors
Authors: Mckimm-Breschkin, J.L. / Sahasrabudhe, A. / Blick, T.J. / Mcdonald, M. / Colman, P.M. / Hart, G.J. / Bethell, R.C. / Varghese, J.N.
History
DepositionApr 7, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: 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 / 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.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_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2758
Polymers43,6961
Non-polymers2,5797
Water6,990388
1
A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,10132
Polymers174,7834
Non-polymers10,31828
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)180.700, 180.700, 180.700
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-989-

CA

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NEURAMINIDASE / SIALIDASE


Mass: 43695.754 Da / Num. of mol.: 1 / Fragment: RESIDUES 82 - 468 / Mutation: R292K (N2-TOKYO/67 NUMBERING) / Source method: isolated from a natural source
Details: INTEGRAL MEMBRANE PROTEIN, MEMBRANE BOUND STALK CLEAVED BY PRONASE, RELEASING FULLY ACTIVE HEAD WITH RESIDUES 82 - 468
Source: (natural) Influenza A virus / Genus: Influenzavirus A
Variant: NEURAMINIDASE R292K MUTATION (N2-TOKYO/3/67 NUMBERING)
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)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]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-g1_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]{}}}[(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-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
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 390 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.81 Å3/Da / Density % sol: 54 %
Description: THIS EXPERIMENT WAS CARRIED OUT TO DETERMINE THE STRUCTURE OF COMPLEX OF NEU5AC2EN AND A DRUG RESISTANT VARIANT OF TERN N9 NEURAMINIDASE GROWN IN PRESENCE OF THE ANTI-INFLUENZA ...Description: THIS EXPERIMENT WAS CARRIED OUT TO DETERMINE THE STRUCTURE OF COMPLEX OF NEU5AC2EN AND A DRUG RESISTANT VARIANT OF TERN N9 NEURAMINIDASE GROWN IN PRESENCE OF THE ANTI-INFLUENZA CARBOXAMIDE DRUG 5-N-ACETYL-4-GUANIDINO -6METHYL(PROPYL) CARBOXAMIDE-4,5-DIHYDRO-2HPYRAN-2-CARBOXYLIC ACID. THE VARIANT HAS A SINGLE R292K MUTATION.
Crystal growpH: 5.9 / Details: 1.9M PHOSPHATE (PH 5.9)
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion / Details: Laver, W.G., (1984) Virology, 137, 314.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mpotassium phosphate1drop
210-15 mg/mlprotein1drop
31.9 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 27, 1996 / Details: YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 35098 / % possible obs: 74.8 % / Observed criterion σ(I): 1 / Redundancy: 4.65 % / Rmerge(I) obs: 0.1 / Rsym value: 0.099
Reflection shellResolution: 1.8→1.863 Å / % possible all: 24
Reflection
*PLUS
Num. measured all: 163196 / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
R-AXISIIdata collection
PROTEINV4data reduction
X-PLOR3model building
X-PLOR3refinement
R-AXISIIdata reduction
PROTEINV. 4data scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TERN N9 R292K MUTANT NEURAMINIDASE

Resolution: 2→6 Å / σ(F): 1 / Details: 2 METAL IONS
RfactorNum. reflection% reflection
Rwork0.166 --
obs0.166 28729 91 %
Refine analyzeLuzzati coordinate error obs: 0.01 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 169 388 3622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.91
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_it2.5
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it3
X-RAY DIFFRACTIONx_scangle_it3.5
LS refinement shellResolution: 2→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.176 1063 -
obs--92 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2CHO.PARTOPCHO.PAR
X-RAY DIFFRACTION3NANA.TOP
X-RAY DIFFRACTION4TOPHPEP

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