SAXSdb — 9ytf

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1. Structure Basics

entry_id	9ytf
deposition_date	2025-10-20
title	TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
keywords	HLA, TCR mimic antibody, de novo design, immune complex, IMMUNE SYSTEM; 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	38.96 Å
rg_electron	39.48 Å
i0	172897000.00
molecular_weight	103260.0 kDa
excluded_volume	127870 Å³
envelope_volume	177180 Å³
shell_volume	40950 Å³
envelope_diameter	141.2 Å
shell_rg	40.54 Å
envelope_rg	39.69 Å
shape_rg	39.44 Å
total_rg	39.68 Å
total_atoms	7270
n_residues	932
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	137.3 Å
rg_real	39.56 Å
rg_real_error	1.42 Å
i0_real	1.7290e+08
i0_real_error	2.8800e+06
rg_reciprocal	39.19 Å
i0_reciprocal	172800000.0000
total_estimate	0.8006
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.5 Å
skewness	0.605
kurtosis	-0.282
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	18260000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.686; Smooth: 0.689

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	MHC class I antigen
formula_weight	31734.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7270

GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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	Homo sapiens

Entity 3 polymer

description	Melanoma-associated antigen 3
formula_weight	1043.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

EVDPIGHLY

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	AD01-VHH
formula_weight	12449.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYGDSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	vAB30 light chain
formula_weight	22793.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

QVQLVQSGAEVKKPGSSVKVSCKASGGSIADGYISWVRQAPGQGLEWMGGILPRVQYTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSPTATAAALKIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Cricetulus griseus

Entity 6 polymer

description	vAB30 heavy chain
formula_weight	23497.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

DIQMTQSPSTLSASVGDRVTITCRASRDIGRYLAWYQQKPGKAPKLLIYLSSSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYSIANQLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Cricetulus griseus

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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	—

resolution	2.60 Å
resolution_method	—
num_particles	1317109

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

TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)