2FD6

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

PDB DOI: https://doi.org/10.2210/pdb2FD6/pdb

Classification: IMMUNE SYSTEM, HYDROLASE
Organism(s): Homo sapiens, Mus musculus
Expression System: Drosophila
Mutation(s): No

Deposited: 2005-12-13 Released: 2006-02-21
Deposition Author(s): Huang, M., Huai, Q., Li, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.276
R-Value Work: 0.239
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 92.83 kDa
Atom Count: 6,600
Modelled Residue Count: 797
Deposited Residue Count: 825
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A	122	Homo sapiens	Mutation(s): 0 EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens) Explore P00749 Go to UniProtKB: P00749
PHAROS: P00749 GTEx: ENSG00000122861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L chain of Fab of ATN-615 anti-uPAR antibody	B [auth L]	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q52L64 (Mus musculus) Explore Q52L64 Go to UniProtKB: Q52L64
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q52L64
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H chain of Fab of ATN-615 anti-uPAR antibody	C [auth H]	213	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q924Q0 (Mus musculus) Explore Q924Q0 Go to UniProtKB: Q924Q0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q924Q0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator surface receptor	D [auth U]	276	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q03405 (Homo sapiens) Explore Q03405 Go to UniProtKB: Q03405
PHAROS: Q03405 GTEx: ENSG00000011422
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03405
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth B]	2		N-Glycosylation	Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	2		N-Glycosylation	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDG Query on NDG Download Ideal Coordinates CCD File SDF format, chain N [auth U] MOL2 format, chain N [auth U]	N [auth U]	2-acetamido-2-deoxy-alpha-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-PVFLNQBWSA-N		Interactions Focus chain N [auth U] Interactions & Density Focus chain N [auth U]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain O [auth U] MOL2 format, chain O [auth U]	O [auth U]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth U] Interactions & Density Focus chain O [auth U]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain M [auth H] MOL2 format, chain M [auth H]	M [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth H] Interactions & Density Focus chain M [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ETX Query on ETX Download Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain J [auth L] SDF format, chain K [auth H] MOL2 format, chain H [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth H]	H [auth L], J [auth L], K [auth H]	2-ETHOXYETHANOL C₄ H₁₀ O₂ ZNQVEEAIQZEUHB-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain J [auth L] Focus chain K [auth H] Interactions & Density Focus chain H [auth L] Focus chain J [auth L] Focus chain K [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain L [auth H] MOL2 format, chain I [auth L] MOL2 format, chain L [auth H]	I [auth L], L [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain L [auth H] Interactions & Density Focus chain I [auth L] Focus chain L [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.276
R-Value Work: 0.239
R-Value Observed: 0.239
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.792	α = 90
b = 86.805	β = 94.54
c = 124.69	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-02-21

Deposition Author(s):

Huang, M.

Huai, Q.

Li, Y.

Revision History (Full details and data files)

Version 1.0: 2006-02-21
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2012-07-18
Changes: Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary