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9yp2

Structure of HaCV P domain in complex with Nanobody 7

Method: X-RAY DIFFRACTION D_max: 95.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

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

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	29.25 Å
rg_electron	28.24 Å
i0	135680000.00
molecular_weight	91163.0 kDa
excluded_volume	113440 Å³
envelope_volume	137720 Å³
shell_volume	39943 Å³
envelope_diameter	105.1 Å
shell_rg	36.03 Å
envelope_rg	28.62 Å
shape_rg	28.20 Å
total_rg	29.04 Å
total_atoms	6441
n_residues	871
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	95.3 Å
rg_real	29.15 Å
rg_real_error	0.70 Å
i0_real	1.3570e+08
i0_real_error	2.1230e+06
rg_reciprocal	29.19 Å
i0_reciprocal	135700000.0000
total_estimate	0.8906
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.1 Å
skewness	0.245
kurtosis	-0.329
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	42290000.0000
n_real_points	55
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Capsid protein
formula_weight	35034.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6812

SRTVESASPAGLLTTPVLTGAGSDNRWGAQIVALQPVPSGFSTCNRHWNLNGSTFGWSSPRFSDIDHPRGNASYTGTGSTNVIETWYANTGTATNNPISNIAPDGFPDMGAIGFSGQTIPTGGWVGFGEVWNVANGSPYNGTVQAYELGFATGAPNSINPATTTVGTQIVAKSIYGVAIGQNQQTAGLFVLSTGIVSTSGPNATTYTPQPNSIVVAPGTPAAAPIGRNVPVMFSGVIRRAGDINAGAGSVNGTQYGVGSQPISVTLQLSLTNYSSSLQPGQFFVWQLNFASGFLEIGLNVDGYFYIGAGASSNMIELTELIDVRPVGVRPNTSTLVFNL

Source

organism	Hare calicivirus
ncbi_taxonomy_id	1743398
host_organism	Escherichia coli

Entity 2 polymer

description	Nanobody 7
formula_weight	12109.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

QVQLQESGGGLVQAGGSLRLSCTASRSIFTYFGKAWYRQAPGKERELVASITSGDTTNYADSVKGRFTISRDAAKNTVYLQMNSLKPDDTAVYYCKYGSYWGQGTQVTVSS

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	365

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6. Citations (1)

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length_a	214.250 Å
length_b	73.510 Å
length_c	59.250 Å
angle_alpha	90.00 °
angle_beta	94.11 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.090 Å
resolution_low	29.660 Å
r_factor	0.1837
r_work	0.1817
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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)