1YWH Hydrolase Receptor date Feb 18, 2005
title Crystal Structure Of Urokinase Plasminogen Activator Recepto
authors P.Llinas, M.H.Le Du, H.Gardsvoll, K.Dano, M.Ploug, B.Gilquin, E.A. A.Menez
compound source
Molecule: Urokinase Plasminogen Activator Surface Receptor
Chain: A, C, E, G, I, K, M, O
Synonym: Upar, U- Par, Monocyte Activation Antigen Mo3, Cd8
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plaur, Mo3, Upar
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtc-Supar

Molecule: Antagonist Peptide
Chain: B, D, F, H, J, L, N, P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.245 R_Free 0.315
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.928 136.831 140.536 90.00 97.27 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand ALC, BMA, DLY, DSN, FUC, MAN, NAG, NDG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, O, M, C, K, I, G, E


Primary referenceCrystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide., Llinas P, Helene Le Du M, Gardsvoll H, Dano K, Ploug M, Gilquin B, Stura EA, Menez A, EMBO J 2005 Apr 7;. PMID:15861141
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (381 Kb) [Save to disk]
  • Biological Unit Coordinates (1ywh.pdb1.gz) 364 Kb
  • Biological Unit Coordinates (1ywh.pdb2.gz) 185 Kb
  • Biological Unit Coordinates (1ywh.pdb3.gz) 186 Kb
  • LPC: Ligand-Protein Contacts for 1YWH
  • CSU: Contacts of Structural Units for 1YWH
  • Likely Quarternary Molecular Structure file(s) for 1YWH
  • Structure Factors (768 Kb)
  • Retrieve 1YWH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YWH from S2C, [Save to disk]
  • Re-refined 1ywh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YWH in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1YWH
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YWH, from MSDmotif at EBI
  • Fold representative 1ywh from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ywh_D] [1ywh_H] [1ywh_I] [1ywh_L] [1ywh] [1ywh_O] [1ywh_E] [1ywh_M] [1ywh_F] [1ywh_B] [1ywh_A] [1ywh_K] [1ywh_J] [1ywh_C] [1ywh_P] [1ywh_G] [1ywh_N]
  • SWISS-PROT database: [Q03405]
  • Domain organization of [UPAR_HUMAN] by SWISSPFAM
  • Domain found in 1YWH: [LU ] by SMART
  • Other resources with information on 1YWH
  • Community annotation for 1YWH at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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