1YWH

crystal structure of urokinase plasminogen activator receptor

PDB DOI: https://doi.org/10.2210/pdb1YWH/pdb

Classification: HYDROLASE RECEPTOR
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2005-02-18 Released: 2005-05-10
Deposition Author(s): Llinas, P., Le Du, M.H., Gardsvoll, H., Dano, K., Ploug, M., Gilquin, B., Stura, E.A., Menez, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.315
R-Value Work: 0.245
R-Value Observed: 0.249

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 304.71 kDa
Atom Count: 18,552
Modelled Residue Count: 2,193
Deposited Residue Count: 2,608
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase plasminogen activator surface receptor	A, C, E, G, I A, C, E, G, I, K, M, O	313	Homo sapiens	Mutation(s): 0 Gene Names: PLAUR, MO3, 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

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antagonist peptide	B, D, F, H, J B, D, F, H, J, L, N, P	13	N/A	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], Q, S, T	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain Q Focus chain S Focus chain T Interactions & Density Focus chain BA [auth b] Focus chain Q Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], DA [auth d], GA [auth g], R, U, AA [auth a], DA [auth d], GA [auth g], R, U, V, X, Y	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain R Focus chain U Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain GA [auth g] Focus chain R Focus chain U Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	FA [auth f], W	2		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain W Interactions & Density Focus chain FA [auth f] Focus chain W
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], EA [auth e], HA [auth h], Z	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain Z Interactions & Density Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain Z
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 BB [auth I] SDF format, chain FB [auth K] SDF format, chain JA [auth A] SDF format, chain GB [auth K] SDF format, chain IA [auth A] SDF format, chain JB [auth M] SDF format, chain MB [auth O] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain SA [auth E] SDF format, chain WA [auth G] MOL2 format, chain BB [auth I] MOL2 format, chain FB [auth K] MOL2 format, chain JA [auth A] MOL2 format, chain GB [auth K] MOL2 format, chain IA [auth A] MOL2 format, chain JB [auth M] MOL2 format, chain MB [auth O] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain SA [auth E] MOL2 format, chain WA [auth G]	BB [auth I] FB [auth K] GB [auth K] IA [auth A] JA [auth A] BB [auth I], FB [auth K], GB [auth K], IA [auth A], JA [auth A], JB [auth M], MB [auth O], NA [auth C], OA [auth C], SA [auth E], WA [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BB [auth I] Focus chain FB [auth K] Focus chain GB [auth K] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JB [auth M] Focus chain MB [auth O] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain SA [auth E] Focus chain WA [auth G] Interactions & Density Focus chain BB [auth I] Focus chain FB [auth K] Focus chain GB [auth K] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain JB [auth M] Focus chain MB [auth O] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain SA [auth E] Focus chain WA [auth G]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain HB [auth K] SDF format, chain QA [auth C] SDF format, chain YA [auth G] SDF format, chain AB [auth G] SDF format, chain CB [auth I] SDF format, chain DB [auth I] SDF format, chain EB [auth I] SDF format, chain IB [auth K] SDF format, chain KA [auth A] SDF format, chain KB [auth M] SDF format, chain LA [auth A] SDF format, chain LB [auth M] SDF format, chain MA [auth A] SDF format, chain NB [auth O] SDF format, chain PA [auth C] SDF format, chain RA [auth C] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain VA [auth E] SDF format, chain XA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain HB [auth K] MOL2 format, chain QA [auth C] MOL2 format, chain YA [auth G] MOL2 format, chain AB [auth G] MOL2 format, chain CB [auth I] MOL2 format, chain DB [auth I] MOL2 format, chain EB [auth I] MOL2 format, chain IB [auth K] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth M] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth M] MOL2 format, chain MA [auth A] MOL2 format, chain NB [auth O] MOL2 format, chain PA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain VA [auth E] MOL2 format, chain XA [auth G] MOL2 format, chain ZA [auth G]	AB [auth G] CB [auth I] DB [auth I] EB [auth I] HB [auth K] AB [auth G], CB [auth I], DB [auth I], EB [auth I], HB [auth K], IB [auth K], KA [auth A], KB [auth M], LA [auth A], LB [auth M], MA [auth A], NB [auth O], PA [auth C], QA [auth C], RA [auth C], TA [auth E], UA [auth E], VA [auth E], XA [auth G], YA [auth G], ZA [auth G]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth G] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain KA [auth A] Focus chain KB [auth M] Focus chain LA [auth A] Focus chain LB [auth M] Focus chain MA [auth A] Focus chain NB [auth O] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth G] Focus chain CB [auth I] Focus chain DB [auth I] Focus chain EB [auth I] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain KA [auth A] Focus chain KB [auth M] Focus chain LA [auth A] Focus chain LB [auth M] Focus chain MA [auth A] Focus chain NB [auth O] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain TA [auth E] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALC Query on ALC	B, D, F, H, J B, D, F, H, J, L, N, P	L-PEPTIDE LINKING	C₉ H₁₇ N O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.315
R-Value Work: 0.245
R-Value Observed: 0.249
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.928	α = 90
b = 136.831	β = 97.27
c = 140.536	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-05-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-05-10
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2018-01-31
Changes: Experimental preparation
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary