SAXSdb — 3u74

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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 Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain U； UniProt 23–305	Not recorded	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 × 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

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 3U74	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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 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 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 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
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 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 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 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 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
9YC5 Human uPAR bound to the Fab fragment of targeted cancer therapeutic antibody FL1 Deposited 2025-09-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 23–305（283 aa）	Not recorded	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
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 ligand/ion Different experimental method Different experimental conditions 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 U； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3u74
Deposition date deposition_date	2011-10-13
Structure title title	Crystal structure of stabilized human uPAR mutant
Keywords keywords	glycosylation, HYDROLASE RECEPTOR; HYDROLASE RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.54 Å
Radius of gyration Rg (electron density) rg_electron	19.66 Å
Forward intensity I(0) i0	19699100.00
Molecular weight molecular_weight	29830.0 kDa
Excluded volume excluded_volume	35749 Å³
Envelope volume envelope_volume	44376 Å³
Hydration-shell volume shell_volume	19019 Å³
Envelope diameter envelope_diameter	63.3 Å
Shell Rg shell_rg	25.68 Å
Envelope Rg envelope_rg	19.71 Å
Shape Rg shape_rg	19.66 Å
Total Rg total_rg	20.46 Å
Total atoms total_atoms	2059
Residues n_residues	263
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

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

Maximum dimension Dmax dmax	65.7 Å
Rg (real space) rg_real	20.44 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.9700e+07
I(0) uncertainty (real space) i0_real_error	2.5620e+05
Rg (reciprocal space) rg_reciprocal	20.46 Å
I(0) (reciprocal space) i0_reciprocal	19700000.0000
Solution quality estimate total_estimate	0.7077
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.605
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2093000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 0.138; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Urokinase plasminogen activator surface receptor
Molecular weight formula_weight	31455.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U
Atom count atom_count	2081

LRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTCSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMCHIDVSCCTKSGCNHPDLDVQYRSG

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 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3u74u1
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.0 — automated matches

Domain ID domain_id	d3u74u2
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.0 — automated matches

Domain ID domain_id	d3u74u3
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3u74U01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3u74U02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3u74U03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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8. Citations (1)

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Unit-cell length a length_a	111.235 Å
Unit-cell length b length_b	111.235 Å
Unit-cell length c length_c	78.571 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	33.040 Å
R factor r_factor	0.2140
R_work r_work	0.2130
R_free r_free	0.2520

fit	/app/data/saxs_computation/u7/3u74/3u74.fit
pddf	/app/data/pr_computation/u7/3u74/3u74.pr.out
profile	/app/data/saxs_computation/u7/3u74/3u74.dat

Crystal structure of stabilized human uPAR mutant

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

Refinement Refinement

Diffraction experiment Diffraction