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9yc6

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

Method: ELECTRON MICROSCOPY D_max: 114.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yc6
deposition_date	2025-09-18
title	Mutant human uPAR bound to the Fab fragment of the 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	35.71 Å
rg_electron	35.94 Å
i0	108714000.00
molecular_weight	78920.0 kDa
excluded_volume	96860 Å³
envelope_volume	133080 Å³
shell_volume	34230 Å³
envelope_diameter	121.6 Å
shell_rg	38.15 Å
envelope_rg	35.62 Å
shape_rg	35.86 Å
total_rg	36.35 Å
total_atoms	10788
n_residues	709
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	114.2 Å
rg_real	36.13 Å
rg_real_error	1.18 Å
i0_real	1.0870e+08
i0_real_error	1.9580e+06
rg_reciprocal	35.87 Å
i0_reciprocal	108700000.0000
total_estimate	0.7865
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	33.7 Å
skewness	0.552
kurtosis	-0.464
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	5898000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.751; Smooth: 0.032

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 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
atom_count	10788

DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source

organism	Mus musculus
common_name	Mouse
ncbi_taxonomy_id	10090
host_organism	Mus musculus

Entity 2 polymer

description	Urokinase plasminogen activator surface receptor
formula_weight	31455.4 kDa
mutation	H47C, N259C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	U

LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTCSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMCHIDVSCCTKSGCNHPDLDVQYRSG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Drosophila melanogaster

Entity 3 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 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 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	syn
entity_count	1

Entity 6 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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resolution	4.80 Å
resolution_method	—
num_particles	86404

fit	/app/data/saxs_computation/yc/9yc6/9yc6.fit
pddf	/app/data/pr_computation/yc/9yc6/9yc6.pr.out
profile	/app/data/saxs_computation/yc/9yc6/9yc6.dat

Mutant human uPAR bound to the Fab fragment of the 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

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)