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- PDB-1vcj: Influenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-... -

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Basic information

Entry
Database: PDB / ID: 1vcj
TitleInfluenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-pentylamino)phenyl)-5-aminomethyl-5-hydroxymethyl-pyrrolidin-2-one
ComponentsNEURAMINIDASE
KeywordsHYDROLASE / neuraminidase / benzoic acid inhibitors / small molecule inhibitor / protein-inhibitor complex
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
Chem-IBA / Neuraminidase
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLommer, B.S. / Ali, S.M. / Bajpai, S.N. / Brouillette, W.J. / Air, G.M. / Luo, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: A benzoic acid inhibitor induces a novel conformational change in the active site of Influenza B virus neuraminidase.
Authors: Lommer, B.S. / Ali, S.M. / Bajpai, S.N. / Brouillette, W.J. / Air, G.M. / Luo, M.
History
DepositionMar 9, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 23, 2004ID: 1UJA
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 5, 2011Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6812
Polymers43,3311
Non-polymers3491
Water1,910106
1
A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules

A: NEURAMINIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,7238
Polymers173,3254
Non-polymers1,3984
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area17840 Å2
ΔGint-79 kcal/mol
Surface area44850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)124.360, 124.360, 71.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein NEURAMINIDASE


Mass: 43331.234 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 78-466 / Source method: isolated from a natural source / Source: (natural) Influenza B virus (B/Lee/40) / Genus: Influenzavirus B / Species: Influenza B virus / Strain: B-LEE-40 / References: UniProt: P03474, exo-alpha-sialidase
#2: Chemical ChemComp-IBA / 4-[(2R)-2-(AMINOMETHYL)-2-(HYDROXYMETHYL)-5-OXOPYRROLIDIN-1-YL]-3-[(1-ETHYLPROPYL)AMINO]BENZOIC ACID / 1-(4-CARBOXY-2-(3-PENTYLAMINO)PHENYL)-5-AMINOMETHYL-5-HYDROXYMETHYL-PYRROLIDIN-2-ONE


Mass: 349.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 3.12 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 3350, sodium chloride, sodium nitrate, calcium chloride, sodium azide, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Sudbeck, E.A., (1997) J. Mol. Biol., 267, 584.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.0 mg/mlprotein1drop
218.5 %(w/v)PEG33501reservoir
30.15 M1reservoirNaCl
42 M1reservoirNaNO3
55 mM1reservoirCaCl2
60.1 %(w/v)sodium azide1reservoirpH6.8

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 6, 1999
RadiationMonochromator: graphite monochromator, 0.3 mm pinhole collimator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 20397 / Num. obs: 18434 / % possible obs: 81.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.084 / Net I/σ(I): 7.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.207 / % possible all: 63.2
Reflection
*PLUS
Highest resolution: 2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 63.2 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
SADIEdata collection
SAINTdata reduction
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→6 Å / Cross valid method: THROUGHUOT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1843 10 %RANDOM
Rwork0.214 ---
obs0.214 18434 --
all-20397 --
Refine analyze
FreeObs
Luzzati coordinate error0.355 Å0.289 Å
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 25 106 3162
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_deg1.689
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
LS refinement shellResolution: 2.4→2.49 Å /
Rfactor% reflection
Rfree0.323 -
Rwork0.294 -
obs-63.2 %
Refinement
*PLUS
Rfactor Rfree: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS

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