2I9B Hydrolase date Sep 05, 2006
title Crystal Structure Of Atf-Urokinase Receptor Complex
authors J.Lubkowski, C.Barinka
compound source
Molecule: Urokinase-Type Plasminogen Activator
Chain: A, B, C, D
Fragment: Atf, Residues 21-163
Ec: 3.4.21.73
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plau
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_strain: Schneider'S S2 Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtbipv5-His

Molecule: Urokinase Plasminogen Activator Surface Receptor
Chain: E, F, G, H
Fragment: Upar, Residues 23-299
Synonym: Upar, U- Par, Monocyte Activation Antigen Mo3, Cd8
Engineered: Yes
Mutation: 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_strain: Schneider'S S2 Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtbipv5-His
symmetry Space Group: P 1 21 1
R_factor 0.222 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.914 281.921 62.811 90.00 105.41 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand BMA, NAG, SO4 enzyme Hydrolase E.C.3.4.21.73 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B, C, D


F, E, H, G


Primary referenceStructural basis of interaction between urokinase-type plasminogen activator and its receptor., Barinka C, Parry G, Callahan J, Shaw DE, Kuo A, Bdeir K, Cines DB, Mazar A, Lubkowski J, J Mol Biol. 2006 Oct 20;363(2):482-95. Epub 2006 Aug 26. PMID:16979660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (248 Kb) [Save to disk]
  • Biological Unit Coordinates (2i9b.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (2i9b.pdb2.gz) 65 Kb
  • Biological Unit Coordinates (2i9b.pdb3.gz) 61 Kb
  • Biological Unit Coordinates (2i9b.pdb4.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 2I9B
  • CSU: Contacts of Structural Units for 2I9B
  • Likely Quarternary Molecular Structure file(s) for 2I9B
  • Structure Factors (742 Kb)
  • Retrieve 2I9B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I9B from S2C, [Save to disk]
  • Re-refined 2i9b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I9B 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 2I9B
  • 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 2I9B, from MSDmotif at EBI
  • Fold representative 2i9b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i9b_C] [2i9b_H] [2i9b] [2i9b_B] [2i9b_F] [2i9b_A] [2i9b_D] [2i9b_G] [2i9b_E]
  • SWISS-PROT database: [Q03405] [P00749]
  • Domain organization of [UPAR_HUMAN] [UROK_HUMAN] by SWISSPFAM
  • Domains found in 2I9B: [EGF] [KR] [LU ] by SMART
  • Other resources with information on 2I9B
  • Community annotation for 2I9B 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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