4K24

Structure of anti-uPAR Fab ATN-658 in complex with uPAR

PDB DOI: https://doi.org/10.2210/pdb4K24/pdb

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

Deposited: 2013-04-08 Released: 2014-02-26
Deposition Author(s): Huang, M.D., Xu, X., Yuan, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.50 Å
R-Value Free: 0.275
R-Value Work: 0.217
R-Value Observed: 0.220

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: 101.42 kDa
Atom Count: 6,771
Modelled Residue Count: 868
Deposited Residue Count: 905
Unique protein chains: 5

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	135	Homo sapiens	Mutation(s): 0 Gene Names: PLAU 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
Vitronectin	B	40	Homo sapiens	Mutation(s): 0 Gene Names: VTN
UniProt & NIH Common Fund Data Resources
Find proteins for P04004 (Homo sapiens) Explore P04004 Go to UniProtKB: P04004
PHAROS: P04004 GTEx: ENSG00000109072
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04004
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-uPAR antibody, heavy chain	C [auth H]	228	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-uPAR antibody, light chain	D [auth L]	219	Mus musculus	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator surface receptor	E [auth U]	283	Homo sapiens	Mutation(s): 0 Gene Names: MO3, PLAUR, UPAR
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: 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], G [auth D]	2		N-Glycosylation	Interactions Focus chain F [auth C] Focus chain G [auth D] Interactions & Density Focus chain F [auth C] Focus chain G [auth D]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth U] MOL2 format, chain I [auth U]	I [auth U]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth U] Interactions & Density Focus chain I [auth U]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain H [auth U] MOL2 format, chain H [auth U]	H [auth U]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain H [auth U] Interactions & Density Focus chain H [auth U]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.50 Å
R-Value Free: 0.275
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 164.659	α = 90
b = 164.659	β = 90
c = 391.582	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-26

Deposition Author(s):

Huang, M.D.

Xu, X.

Yuan, C.

Revision History (Full details and data files)

Version 1.0: 2014-02-26
Type: Initial release
Version 1.1: 2014-03-05
Changes: Data collection
Version 1.2: 2019-12-11
Changes: Advisory, Data collection, Database references, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary