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1vcj

Influenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-pentylamino)phenyl)-5-aminomethyl-5-hydroxymethyl-pyrrolidin-2-one

Method: X-RAY DIFFRACTION Dmax: 62.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NEURAMINIDASE

OrganismNot specified

UniProt P03474

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 78–466 Fragment：CATALYTIC DOMAIN RESIDUES 78-466 IBA 4-[(2R)-2-(AMINOMETHYL)-2-(HYDROXYMETHYL)-5-OXOPYRROLIDIN-1-YL]-3-[(1-ETHYLPROPYL)AMINO]BENZOIC ACID × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；PEG 3350, sodium chloride, sodium nitrate, calcium chloride, sodium azide, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.40 Å R-free 0.255

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1VCJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B9S NOVEL AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE MAKE SELECTIVE INTERACTIONS WITH CONSERVED RESIDUES AND WATER MOLECULES IN THE ACTIVE SITE Deposited 1999-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 77–466（390 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 8 FDI 4-(N-ACETYLAMINO)-3-[N-(2-ETHYLBUTANOYLAMINO)]BENZOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 2.50 Å R-free 0.251
1B9T NOVEL AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE MAKE SELECTIVE INTERACTIONS WITH CONSERVED RESIDUES AND WATER MOLECULES IN THE ACTIVE SITE Deposited 1999-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 77–466（390 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 8 RAI 1-(4-CARBOXY-2-GUANIDINOPENTYL)-5,5'-DI(HYDROXYMETHYL)PYRROLIDIN-2-ONE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 2.40 Å R-free 0.271
1B9V NOVEL AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE MAKE SELECTIVE INTERACTIONS WITH CONSERVED RESIDUES AND WATER MOLECULES IN TEH ACTIVE SITE Deposited 1999-02-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 77–466（390 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 8 RA2 1-[4-CARBOXY-2-(3-PENTYLAMINO)PHENYL]-5,5'-DI(HYDROXYMETHYL)PYRROLIDIN-2-ONE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.8；pH 6.8
Resolution 2.35 Å R-free 0.271
1INF INFLUENZA VIRUS B/LEE/40 NEURAMINIDASE COMPLEXED WITH BANA113 INHIBITOR Deposited 1995-07-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 77–466（390 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 8 ST4 4-(ACETYLAMINO)-3-GUANIDINOBENZOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.40 Å
1INV A SIALIC ACID DERIVED PHOSPHONATE ANALOG INHIBITS DIFFERENT STRAINS OF INFLUENZA VIRUS NEURAMINIDASE WITH DIFFERENT EFFICIENCIES Deposited 1994-09-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 77–466（390 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 8 EQP (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions NATIVE CRYSTALS SOAKED IN 10MM EPANA SOLUTION, PH 7.4.
Resolution 2.40 Å
1IVB STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE Deposited 1994-12-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 77–466（390 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 8 ST1 4-(ACETYLAMINO)-3-HYDROXY-5-NITROBENZOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions NATIVE CRYSTALS SOAKED IN 5MM BANA105 SOLUTION, PH 7.4.
Resolution 2.40 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRAM_INBLE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–389； UniProt 78–466

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1vcj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vcj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vcj
Deposition date deposition_date2004-03-09
Structure title titleInfluenza B virus neuraminidase complexed with 1-(4-Carboxy-2-(3-pentylamino)phenyl)-5-aminomethyl-5-hydroxymethyl-pyrrolidin-2-one
Keywords keywordsneuraminidase, benzoic acid inhibitors, small molecule inhibitor, protein-inhibitor complex, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.42 Å
Radius of gyration Rg (electron density) rg_electron19.46 Å
Forward intensity I(0) i033588000.00
Molecular weight molecular_weight43623.0 kDa
Excluded volume excluded_volume54048 ų
Envelope volume envelope_volume60332 ų
Hydration-shell volume shell_volume24610 ų
Envelope diameter envelope_diameter64.8 Å
Shell Rg shell_rg27.22 Å
Envelope Rg envelope_rg19.89 Å
Shape Rg shape_rg19.46 Å
Total Rg total_rg20.36 Å
Total atoms total_atoms3056
Residues n_residues389
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.5 Å
Rg (real space) rg_real20.26 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real3.3590e+07
I(0) uncertainty (real space) i0_real_error4.2220e+05
Rg (reciprocal space) rg_reciprocal20.29 Å
I(0) (reciprocal space) i0_reciprocal33590000.0000
Solution quality estimate total_estimate0.8217
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9 Å
Skewness Skewness skewness0.090
Kurtosis Kurtosis kurtosis-0.475
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11760000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1vcja_
Class classb — All beta proteins
Fold Fold foldb.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamilyb.68.1 — Sialidases
Family Family familyb.68.1.1 — Sialidases (neuraminidases)

CATH v4.4 (1 domains)

Domain ID domain_id1vcjA00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)