SAXSdb — 9ytd

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1. Structure Basics

entry_id	9ytd
deposition_date	2025-10-20
title	Designed antibody vAB66 targeting PAP-HLA A*02:01
keywords	Fab, complex, immunology, DE NOVO PROTEIN, DE NOVO PROTEIN-IMMUNE SYSTEM complex; DE NOVO PROTEIN/IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

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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	38.15 Å
rg_electron	38.33 Å
i0	170979000.00
molecular_weight	103590.0 kDa
excluded_volume	128630 Å³
envelope_volume	175440 Å³
shell_volume	40900 Å³
envelope_diameter	137.8 Å
shell_rg	40.82 Å
envelope_rg	38.34 Å
shape_rg	38.28 Å
total_rg	38.64 Å
total_atoms	7304
n_residues	926
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	132.2 Å
rg_real	38.56 Å
rg_real_error	1.13 Å
i0_real	1.7100e+08
i0_real_error	2.9290e+06
rg_reciprocal	38.31 Å
i0_reciprocal	170900000.0000
total_estimate	0.8359
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.5 Å
skewness	0.536
kurtosis	-0.313
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	17570000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.813; Smooth: 0.732

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	HLA class I histocompatibility antigen, A alpha chain
formula_weight	32256.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7368

MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Beta-2-microglobulin
formula_weight	11879.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Prostatic acid phosphatase-derived peptide
formula_weight	981.2 kDa
ec_number	3.1.3.2,3.1.3.5,3.1.3.48
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

TLMSAMTNL

Entity 4 polymer

description	AD01 nanobody
formula_weight	13867.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYGDSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSSGAPHHHHHHHH

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Homo sapiens

Entity 5 polymer

description	vAB66 heavy chain
formula_weight	23158.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLQESGPGLVKPSETLSLTCAVSNAKLTEYDWWGWIRQPPGKGLEWIGSGNAYGLVYYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARYDGVVLYPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Cricetulus griseus

Entity 6 polymer

description	vAB66 light chain
formula_weight	23649.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIQMTQSPSSLSASVGDRVTITCRASADPQGFLNWYQQKPGKAPKLLIYLASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSWSERGPYLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Cricetulus griseus

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	64

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.50 Å
resolution_method	—
num_particles	880830

fit	/app/data/saxs_computation/yt/9ytd/9ytd.fit
pddf	/app/data/pr_computation/yt/9ytd/9ytd.pr.out
profile	/app/data/saxs_computation/yt/9ytd/9ytd.dat

Designed antibody vAB66 targeting PAP-HLA A*02:01

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

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)