SAXSdb — 9yc5

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Urokinase plasminogen activator surface receptor

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 23–305	Not recorded	Anti-uPAR antibody FL1 Fab heavy chain × 1 Anti-uPAR antibody FL1 Fab light chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4；20mM Tris, 150mM NaCl, 2.5% Glycerol, 1mM EDTA, pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.94 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9YC5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FD6 Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A Deposited 2005-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain U 23–297（275 aa） Fragment：residues 23-297	Not recorded	SO4 SULFATE ION × 1 ETX 2-ETHOXYETHANOL × 3 EDO 1,2-ETHANEDIOL × 2 PGE TRIETHYLENE GLYCOL × 1 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 6.5；298 K；4% PEG4000, 5% ethylene glycol, 5% methanol, 0.05% sodium azide, 50 mM cacodylate, pH 6.5, MICRODIALYSIS, temperature 298K	Resolution 1.90 Å R-free 0.276
2FD6 Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A Deposited 2005-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain U 23–297（275 aa） Fragment：residues 23-297	Not recorded	SO4 SULFATE ION × 1 ETX 2-ETHOXYETHANOL × 3 EDO 1,2-ETHANEDIOL × 2 PGE TRIETHYLENE GLYCOL × 1 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 6.5；298 K；4% PEG4000, 5% ethylene glycol, 5% methanol, 0.05% sodium azide, 50 mM cacodylate, pH 6.5, MICRODIALYSIS, temperature 298K	Resolution 1.90 Å R-free 0.276
2I9B Crystal structure of ATF-urokinase receptor complex Deposited 2006-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 23–299（277 aa） Fragment：UPAR, residues 23-299	Mutation：N162Q, N172Q, N200Q, N233Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；22.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.265
2I9B Crystal structure of ATF-urokinase receptor complex Deposited 2006-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 23–299（277 aa） Fragment：UPAR, residues 23-299	Mutation：N162Q, N172Q, N200Q, N233Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；22.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.265
2I9B Crystal structure of ATF-urokinase receptor complex Deposited 2006-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 23–299（277 aa） Fragment：UPAR, residues 23-299	Mutation：N162Q, N172Q, N200Q, N233Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；22.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.265
2I9B Crystal structure of ATF-urokinase receptor complex Deposited 2006-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 23–299（277 aa） Fragment：UPAR, residues 23-299	Mutation：N162Q, N172Q, N200Q, N233Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；22.5% w/v PEG3350, 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.265
3BT1 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 23–303（281 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；12% PEG 3350, 50mM HEPES pH 7.5, MICRODIALYSIS, temperature 295K	Resolution 2.80 Å R-free 0.308
3BT2 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain U 23–303（281 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K	Resolution 2.50 Å R-free 0.272
3BT2 Structure of urokinase receptor, urokinase and vitronectin complex Deposited 2007-12-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain U 23–303（281 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.5；295 K；8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K	Resolution 2.50 Å R-free 0.272
3U73 Crystal structure of stabilized human uPAR mutant in complex with ATF Deposited 2011-10-13	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 23–305（283 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；0.2M NaCl, 100mM HEPES, pH7.4, 1.8 M ammonium sulfate, vapor diffusion, sitting drop, temperature 295.0K	Resolution 3.19 Å R-free 0.258
3U74 Crystal structure of stabilized human uPAR mutant Deposited 2011-10-13	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain U 23–305（283 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；100 mM HEPES, pH 7.5, 2% (w/v) PEG400, 2 M ammonium sulfate, vapor diffusion, sitting drop, temperature 295.0K	Resolution 2.39 Å R-free 0.252
4K24 Structure of anti-uPAR Fab ATN-658 in complex with uPAR Deposited 2013-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain U 23–303（281 aa） Fragment：UNP residues 23-303	Not recorded	MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1M HEPES pH 7.5, 55%(v/v) Tacsimate, 2%(v/v) 2-methyl-1,3-propanediol, vapor diffusion, sitting drop, temperature 295K	Resolution 4.50 Å R-free 0.275
4QTI Crystal structure of human uPAR in complex with anti-uPAR Fab 8B12 Deposited 2014-07-08	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 23–305（283 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；48% MPD, 100mM Tris, 100mM NaCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.00 Å R-free 0.296
7E17 Structure of dimeric uPAR Deposited 2021-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–299（277 aa） Chain B 23–299（277 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；1.8-2.2 M ammonium sulphate in 50 mM sodium acetate at pH 4.5oC5.2	Resolution 2.96 Å R-free 0.299
7V63 Structure of dimeric uPAR at low pH Deposited 2021-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–299（277 aa） Chain B 23–299（277 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；1.8-2.2 M ammonium sulphate in 50 mM sodium acetate at pH 4.5-5.2	Resolution 2.91 Å R-free 0.273
9YC6 Mutant human uPAR bound to the Fab fragment of the targeted cancer therapeutic antibody FL1 Deposited 2025-09-18	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain U 23–305（283 aa）	Mutation：H47C, N259C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20mM Tris, 150mM NaCl, 2.5% Glycerol, 1mM EDTA, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UPAR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–283； UniProt 23–305

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yc5
Deposition date deposition_date	2025-09-18
Structure title title	Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1
Keywords keywords	Complex, Targeted cancer therapy, Monoclonal anti-uPAR antibody FL1, Antibody-drug conjugate, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.63 Å
Radius of gyration Rg (electron density) rg_electron	33.68 Å
Forward intensity I(0) i0	77822200.00
Molecular weight molecular_weight	66963.0 kDa
Excluded volume excluded_volume	82401 Å³
Envelope volume envelope_volume	111320 Å³
Hydration-shell volume shell_volume	30835 Å³
Envelope diameter envelope_diameter	117.8 Å
Shell Rg shell_rg	36.31 Å
Envelope Rg envelope_rg	33.64 Å
Shape Rg shape_rg	33.60 Å
Total Rg total_rg	34.12 Å
Total atoms total_atoms	9157
Residues n_residues	606
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	116.9 Å
Rg (real space) rg_real	34.01 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	7.7820e+07
I(0) uncertainty (real space) i0_real_error	1.2550e+06
Rg (reciprocal space) rg_reciprocal	33.77 Å
I(0) (reciprocal space) i0_reciprocal	77810000.0000
Solution quality estimate total_estimate	0.5851
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.3 Å
Skewness Skewness skewness	0.596
Kurtosis Kurtosis kurtosis	-0.324
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5826000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.677; Stabil: 1.000; Sysdev: 0.078; Positv: 1.000; Valcen: 0.523; Smooth: 0.812

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Urokinase plasminogen activator surface receptor
Molecular weight formula_weight	31501.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9157

LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	Anti-uPAR antibody FL1 Fab heavy chain
Molecular weight formula_weight	23581.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLQQSGSVLVRPGTSVNLSCKASGYTFTSYWMSWVKQRPGQGLEWIGEIFPKSGRINSNENFRGKATLTVDTSSSTAYINLSSLTSEDSAVYYCSPIYSGDYGFADWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	Anti-uPAR antibody FL1 Fab light chain
Molecular weight formula_weight	24168.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQTPLSLPVSLGDQASISCRSSQSVVSNNGKTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPWTFGGGTKLEVKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 4 Entity 4 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.94 Å
Resolution测定方法 resolution_method	—
颗粒数 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Urokinase plasminogen activator surface receptor

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)