1ncd

REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX

Method: X-RAY DIFFRACTION Dmax: 119.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

INFLUENZA A SUBTYPE N9 NEURAMINIDASE

OrganismNot specified

UniProt P05803

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 12 其他Polymer 8 PDB declaration: dodecameric(12) Consistent with protein copy count Chain N; UniProt 83–470 Not recorded IGG2A-KAPPA NC41 FAB (LIGHT CHAIN) × 4 IGG2A-KAPPA NC41 FAB (HEAVY CHAIN) × 4 (P01865) ;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 ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRAM_IAWHM
Isoform
PDB entities 1
Chains and sequence ranges Author chain N; PDBConstruct 2–389; UniProt 83–470

IGG2A-KAPPA NC41 FAB (HEAVY CHAIN)

OrganismNot specified

UniProt P01865

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 12 其他Polymer 8 PDB declaration: dodecameric(12) Consistent with protein copy count Chain H; UniProt 1–101 Not recorded INFLUENZA A SUBTYPE N9 NEURAMINIDASE × 4 (P05803) IGG2A-KAPPA NC41 FAB (LIGHT CHAIN) × 4 ;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 ; × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.90 Å

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.

31 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GCAM_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain H; PDBConstruct 121–221; UniProt 1–101

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 1ncd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ncd
Deposition date deposition_date1992-01-21
Structure title titleREFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX
Keywords keywordsHYDROLASE(O-GLYCOSYL); HYDROLASE(O-GLYCOSYL)
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.41
Radius of gyration Rg (electron density) rg_electron34.36
Forward intensity I(0) i0143013000.00
Molecular weight molecular_weight92766.0 kDa
Excluded volume excluded_volume114640 ų
Envelope volume envelope_volume147310 ų
Hydration-shell volume shell_volume38036 ų
Envelope diameter envelope_diameter123.9
Shell Rg shell_rg38.38
Envelope Rg envelope_rg34.66
Shape Rg shape_rg34.31
Total Rg total_rg34.82
Total atoms total_atoms6516
Residues n_residues814
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax119.2
Rg (real space) rg_real34.75
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real1.4300e+08
I(0) uncertainty (real space) i0_real_error2.4900e+06
Rg (reciprocal space) rg_reciprocal34.54
I(0) (reciprocal space) i0_reciprocal143000000.0000
Solution quality estimate total_estimate0.8043
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1
Skewness Skewness skewness0.600
Kurtosis Kurtosis kurtosis-0.301
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22120000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.632; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.803; Smooth: 0.753

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1ncdh1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1ncdh2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1ncdl1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd1ncdl2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd1ncdn_
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 (5 domains)

Domain ID domain_id1ncdH01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ncdH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ncdL01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ncdL02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1ncdN00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10

8. Citations (4)

9. Files and Curves (10)