5kuy

Influenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with designed inhibitor protein HSB.2A

Method: X-RAY DIFFRACTION Dmax: 153.9 Å Quality: GOOD

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

Hemagglutinin HA1

Influenza A virus (strain A/Hong Kong/1/1968 H3N2)

UniProt Q91MA7

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 × 9 其他Polymer 6 PDB declaration: nonameric(9) Consistent with protein copy count Chain A; UniProt 27–345 Chain B; UniProt 346–521 Chain C; UniProt 27–345 Chain D; UniProt 346–521 Chain E; UniProt 27–345 Chain F; UniProt 346–521 Mutation:R452G Designed influenza inhibitor HSB.2A × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293.15 K;10% PEG 6000, 100 mM MES pH 6.0 Resolution 2.60 Å R-free 0.204

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.

46 other PDB entries and 90 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMA_I68A4
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain A; PDBConstruct 5–323; UniProt 27–345 Author chain C; PDBConstruct 5–323; UniProt 27–345 Author chain E; PDBConstruct 5–323; UniProt 27–345 Author chain B; PDBConstruct 1–176; UniProt 346–521 Author chain D; PDBConstruct 1–176; UniProt 346–521 Author chain F; PDBConstruct 1–176; UniProt 346–521

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 5kuy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5kuy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5kuy
Deposition date deposition_date2016-07-13
Structure title titleInfluenza hemagglutinin H3 A/Hong Kong/1/1968 in complex with designed inhibitor protein HSB.2A
Keywords keywordsInfluenza, inhibitor, complex, design, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier44.65
Radius of gyration Rg (electron density) rg_electron44.46
Forward intensity I(0) i0575720000.00
Molecular weight molecular_weight191830.0 kDa
Excluded volume excluded_volume237710 ų
Envelope volume envelope_volume317890 ų
Hydration-shell volume shell_volume61965 ų
Envelope diameter envelope_diameter166.5
Shell Rg shell_rg46.05
Envelope Rg envelope_rg44.92
Shape Rg shape_rg44.46
Total Rg total_rg44.53
Total atoms total_atoms13497
Residues n_residues1693
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 dmax153.9
Rg (real space) rg_real44.94
Rg uncertainty (real space) rg_real_error2.22
I(0) (real space) i0_real5.7570e+08
I(0) uncertainty (real space) i0_real_error1.2770e+07
Rg (reciprocal space) rg_reciprocal44.66
I(0) (reciprocal space) i0_reciprocal575500000.0000
Solution quality estimate total_estimate0.8421
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.0
Skewness Skewness skewness0.483
Kurtosis Kurtosis kurtosis-0.422
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57930000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.799

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5kuyA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id5kuyB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5kuyC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id5kuyD00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10
Domain ID domain_id5kuyE01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology209 — Hemagglutinin (Ha1 Chain); Chain: A; domain 1
Homologous superfamily homologous superfamily20 — Haemagglutinin, alpha/beta domain, HA1 chain
Domain ID domain_id5kuyF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology20 — Hemagglutinin Ectodomain; Chain B
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)