2fd6

Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A

Method: X-RAY DIFFRACTION

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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 4 其他Polymer 2	L chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q52L64） H chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q4V9V8） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 2	L chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q52L64） H chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q4V9V8） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	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 1–122； UniProt 31–152

L chain of Fab of ATN-615 anti-uPAR antibody

OrganismNot specified

UniProt Q52L64

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 2	Urokinase-type plasminogen activator × 1 （P00749） H chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q4V9V8） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 2	Urokinase-type plasminogen activator × 1 （P00749） H chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q4V9V8） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q52L64_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 26–211； UniProt 46–239

H chain of Fab of ATN-615 anti-uPAR antibody

OrganismNot specified

UniProt Q4V9V8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 2	Urokinase-type plasminogen activator × 1 （P00749） L chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q52L64） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 2	Urokinase-type plasminogen activator × 1 （P00749） L chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q52L64） Urokinase plasminogen activator surface receptor × 1 （Q03405） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4V9V8_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 2–197； UniProt 21–223

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 4 其他Polymer 2	Urokinase-type plasminogen activator × 1 （P00749） L chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q52L64） H chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q4V9V8） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 2	Urokinase-type plasminogen activator × 1 （P00749） L chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q52L64） H chain of Fab of ATN-615 anti-uPAR antibody × 1 （Q4V9V8） alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SULFATE ION × 1 2-ETHOXYETHANOL × 3 1,2-ETHANEDIOL × 2 TRIETHYLENE GLYCOL × 1 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 TETRAETHYLENE GLYCOL × 1 water × 4	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	4
Chains and sequence ranges	Author chain U； PDBConstruct 3–276； UniProt 23–297

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	2fd6
Deposition date deposition_date	2005-12-13
Structure title title	Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A
Keywords keywords	uPAR, ATF, ATN-615 antibody, Fab, ternary complex, IMMUNE SYSTEM, HYDROLASE; IMMUNE SYSTEM, HYDROLASE
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.

2fd6__assembly_1__model_1

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

Download this curve (.dat)

2fd6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fd6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.09 Å
Rg (electron density)	39.92 Å
Total Rg	39.98 Å
Atom count	6264
Residues	797
Excluded volume	110060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fd6__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2fd6__assembly_2__model_1`	tetrameric （4）	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 (13)

Entity 1 Entity 1 polymer

Description description	Urokinase-type plasminogen activator
Molecular weight formula_weight	13892.8 kDa
EC 编号 ec_number	3.4.21.73
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	6600

CDCLNGGTCVSNKYFSNIHWCNCPKKFGGQHCEIDKSKTCYEGNGHFYRGKASTDTMGRPCLPWNSATVLQQTYHAHRSDALQLGLGKHNYCRNPDNRRRPWCYVQVGLKPLVQECMVHDCA

Source Source

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

Entity 2 Entity 2 polymer

Description description	L chain of Fab of ATN-615 anti-uPAR antibody
Molecular weight formula_weight	23437.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVLTQSPDITAASLGQKVTITCSASSSVSYMHWYQQKSGTSPKPWIFEISKLASGVPARFSGSGSGTSYSLTISSMEAEDAAIYYCQQWNYPFTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEAKA

Entity 3 Entity 3 polymer

Description description	H chain of Fab of ATN-615 anti-uPAR antibody
Molecular weight formula_weight	22984.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GVKLQQSGPEVVKPGASVKISCKASGYSFTNFYIHWVKQRPGQGLEWIGWIFHGSDNTEYNEKFKDKATLTADTSSSTAYMQLSSLTSEDSAVYFCARWGPHWYFDVWGQGTTVTVSSAKTTPPSVYPLAPGNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIAAA

Entity 4 Entity 4 polymer

Description description	Urokinase plasminogen activator surface receptor
Molecular weight formula_weight	30668.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

SLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPD

Source Source

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

Entity 5 Entity 5 branched

Description description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2-ETHOXYETHANOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

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

Entity 12 Entity 12 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	336

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2fd6a1
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.3.11.0 — automated matches

Domain ID domain_id	d2fd6a2
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	d2fd6h1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2fd6h2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2fd6l1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2fd6l2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2fd6u1
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	d2fd6u2
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	d2fd6u3
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 (9 domains)

Domain ID domain_id	2fd6A01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

Domain ID domain_id	2fd6A02
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	2fd6H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2fd6H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2fd6L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2fd6L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2fd6U01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	2fd6U02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	2fd6U03
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	51.792 Å
Unit-cell length b length_b	86.805 Å
Unit-cell length c length_c	124.690 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	41.360 Å
R factor r_factor	0.2390
R_work r_work	0.2390
R_free r_free	0.2760

Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor and an anti-upar antibody at 1.9 A

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

L chain of Fab of ATN-615 anti-uPAR antibody

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H chain of Fab of ATN-615 anti-uPAR antibody

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

2fd6__assembly_1__model_1

2fd6__assembly_1__model_1 | I(q)

2fd6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (13)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)