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9yc5

Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1

Method: ELECTRON MICROSCOPY D_max: 116.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yc5
deposition_date	2025-09-18
title	Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1
keywords	Complex, Targeted cancer therapy, Monoclonal anti-uPAR antibody FL1, Antibody-drug conjugate, 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	33.63 Å
rg_electron	33.68 Å
i0	77822200.00
molecular_weight	66963.0 kDa
excluded_volume	82401 Å³
envelope_volume	111320 Å³
shell_volume	30835 Å³
envelope_diameter	117.8 Å
shell_rg	36.31 Å
envelope_rg	33.64 Å
shape_rg	33.60 Å
total_rg	34.12 Å
total_atoms	9157
n_residues	606
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	116.9 Å
rg_real	34.01 Å
rg_real_error	1.36 Å
i0_real	7.7820e+07
i0_real_error	1.2550e+06
rg_reciprocal	33.77 Å
i0_reciprocal	77810000.0000
total_estimate	0.5851
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	32.3 Å
skewness	0.596
kurtosis	-0.324
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	5826000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.523; Smooth: 0.812

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Urokinase plasminogen activator surface receptor
formula_weight	31501.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9157

LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Drosophila melanogaster

Entity 2 polymer

description	Anti-uPAR antibody FL1 Fab heavy chain
formula_weight	23581.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

EVQLQQSGSVLVRPGTSVNLSCKASGYTFTSYWMSWVKQRPGQGLEWIGEIFPKSGRINSNENFRGKATLTVDTSSSTAYINLSSLTSEDSAVYYCSPIYSGDYGFADWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Source

organism	Mus musculus
common_name	Mouse
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 3 polymer

description	Anti-uPAR antibody FL1 Fab light chain
formula_weight	24168.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source

organism	Mus musculus
common_name	Mouse
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 4 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

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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	2.94 Å
resolution_method	—
num_particles	184642

fit	/app/data/saxs_computation/yc/9yc5/9yc5.fit
pddf	/app/data/pr_computation/yc/9yc5/9yc5.pr.out
profile	/app/data/saxs_computation/yc/9yc5/9yc5.dat

Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)