SAXSdb — 9yp2

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

Capsid protein

Hare calicivirus

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1983–2321 Chain B； UniProt 1983–2321	Fragment：P domain	Nanobody 7 × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium fluoride, 20% PEG3350	Resolution 2.09 Å R-free 0.223

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A4D6I9J0_9CALI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–339； UniProt 1983–2321 Author chain B； PDBConstruct 1–339； UniProt 1983–2321

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yp2
Deposition date deposition_date	2025-10-13
Structure title title	Structure of HaCV P domain in complex with Nanobody 7
Keywords keywords	Nanobody, complex, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	29.25 Å
Radius of gyration Rg (electron density) rg_electron	28.24 Å
Forward intensity I(0) i0	135680000.00
Molecular weight molecular_weight	91163.0 kDa
Excluded volume excluded_volume	113440 Å³
Envelope volume envelope_volume	137720 Å³
Hydration-shell volume shell_volume	39943 Å³
Envelope diameter envelope_diameter	105.1 Å
Shell Rg shell_rg	36.03 Å
Envelope Rg envelope_rg	28.62 Å
Shape Rg shape_rg	28.20 Å
Total Rg total_rg	29.04 Å
Total atoms total_atoms	6441
Residues n_residues	871
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	95.3 Å
Rg (real space) rg_real	29.15 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.3570e+08
I(0) uncertainty (real space) i0_real_error	2.1230e+06
Rg (reciprocal space) rg_reciprocal	29.19 Å
I(0) (reciprocal space) i0_reciprocal	135700000.0000
Solution quality estimate total_estimate	0.8906
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.1 Å
Skewness Skewness skewness	0.245
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42290000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	35034.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6812

SRTVESASPAGLLTTPVLTGAGSDNRWGAQIVALQPVPSGFSTCNRHWNLNGSTFGWSSPRFSDIDHPRGNASYTGTGSTNVIETWYANTGTATNNPISNIAPDGFPDMGAIGFSGQTIPTGGWVGFGEVWNVANGSPYNGTVQAYELGFATGAPNSINPATTTVGTQIVAKSIYGVAIGQNQQTAGLFVLSTGIVSTSGPNATTYTPQPNSIVVAPGTPAAAPIGRNVPVMFSGVIRRAGDINAGAGSVNGTQYGVGSQPISVTLQLSLTNYSSSLQPGQFFVWQLNFASGFLEIGLNVDGYFYIGAGASSNMIELTELIDVRPVGVRPNTSTLVFNL

来源 Source

来源生物 organism	Hare calicivirus
NCBI Class编号 ncbi_taxonomy_id	1743398
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nanobody 7
Molecular weight formula_weight	12109.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QVQLQESGGGLVQAGGSLRLSCTASRSIFTYFGKAWYRQAPGKERELVASITSGDTTNYADSVKGRFTISRDAAKNTVYLQMNSLKPDDTAVYYCKYGSYWGQGTQVTVSS

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	365

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8. Citations (1)

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Unit-cell length a length_a	214.250 Å
Unit-cell length b length_b	73.510 Å
Unit-cell length c length_c	59.250 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	29.660 Å
R factor r_factor	0.1837
R_work r_work	0.1817
R_free r_free	0.2225

fit	/app/data/saxs_computation/yp/9yp2/9yp2.fit
pddf	/app/data/pr_computation/yp/9yp2/9yp2.pr.out
profile	/app/data/saxs_computation/yp/9yp2/9yp2.dat

Structure of HaCV P domain in complex with Nanobody 7

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

Capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)