SAXSdb — 3bt1

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

Urokinase-type plasminogen activator

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Vitronectin × 1 （P04004） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UROK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–135； UniProt 21–153

Vitronectin

Homo sapiens

UniProt P04004

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Urokinase-type plasminogen activator × 1 （P00749） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VTNC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–40； UniProt 21–60

Urokinase plasminogen activator surface receptor

Homo sapiens

UniProt Q03405

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Urokinase-type plasminogen activator × 1 （P00749） Vitronectin × 1 （P04004） alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UPAR_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain U； PDBConstruct 3–283； UniProt 23–303

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	3bt1
Deposition date deposition_date	2007-12-27
Structure title title	Structure of urokinase receptor, urokinase and vitronectin complex
Keywords keywords	;protein-protein complex, Glycoprotein, GPI-anchor, Lipoprotein, Membrane, Receptor, Secreted, Blood coagulation, EGF-like domain, Fibrinolysis, Hydrolase, Kringle, Phosphoprotein, Plasminogen activation, Protease, Serine protease, Zymogen, Cell adhesion, Heparin-binding, Sulfation, Immunoglobulin domain, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3bt1__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3bt1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bt1__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.60 Å
Rg (electron density)	24.87 Å
Total Rg	25.63 Å
Atom count	3461
Residues	438
Excluded volume	60058 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bt1__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Urokinase-type plasminogen activator
Molecular weight formula_weight	15359.3 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	3461

RSSNELHQVPSNCDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCAD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	Vitronectin
Molecular weight formula_weight	4573.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Urokinase plasminogen activator surface receptor
Molecular weight formula_weight	31601.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

RSLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Drosophila melanogaster

Entity 4 Entity 4 branched

Description description	alpha-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	man
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3bt1a1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d3bt1a2
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d3bt1b_
Class class	g — Small proteins
Fold Fold fold	g.64 — Somatomedin B domain
Superfamily Superfamily superfamily	g.64.1 — Somatomedin B domain
Family Family family	g.64.1.1 — Somatomedin B domain

Domain ID domain_id	d3bt1u1
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.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d3bt1u2
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.7.1.3 — Extracellular domain of cell surface receptors

Domain ID domain_id	d3bt1u3
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.7.1.3 — Extracellular domain of cell surface receptors

CATH v4.4 (5 domains)

Domain ID domain_id	3bt1A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	3bt1A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	3bt1U01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3bt1U02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3bt1U03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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Unit-cell length a length_a	97.353 Å
Unit-cell length b length_b	105.187 Å
Unit-cell length c length_c	55.360 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	27.680 Å
R factor r_factor	0.2440
R_work r_work	0.2410
R_free r_free	0.3080

Structure of urokinase receptor, urokinase and vitronectin complex

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

Urokinase-type plasminogen activator

State in the Current Structure

Other States of the Same Protein in the Database

Vitronectin

State in the Current Structure

Other States of the Same Protein in the Database

Urokinase plasminogen activator surface receptor

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bt1__assembly_1__model_1

3bt1__assembly_1__model_1 | I(q)

3bt1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Structure of urokinase receptor, urokinase and vitronectin complex

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

Urokinase-type plasminogen activator

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Vitronectin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Urokinase plasminogen activator surface receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bt1__assembly_1__model_1

3bt1__assembly_1__model_1 | I(q)

3bt1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (1)