3BT2 Immune System date Dec 27, 2007
title Structure Of Urokinase Receptor, Urokinase And Vitronectin C
authors M.Huang
compound source
Molecule: Urokinase-Type Plasminogen Activator
Chain: A
Fragment: Urokinase Amino Terminal Fragment, Urokinase-Type Plasminogen Activator Long Chain A, Unp Residues 21-153;
Synonym: Upa, U-Plasminogen Activator
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plau
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtbip

Molecule: Vitronectin
Chain: B
Fragment: Sometomedin-B Domain
Synonym: Serum-Spreading Factor, S-Protein, V75
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vtn
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid

Molecule: Anti-Upar Antibody, Light Chain
Chain: L
Fragment: Fab Fragment, Light Chain
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Anti-Upar Antibody, Heavy Chain
Chain: H
Fragment: Fab Fragment, Heavy Chain
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Urokinase Plasminogen Activator Surface Receptor
Chain: U
Synonym: Upar, U-Par, Monocyte Activation Antigen Mo3, Cd87
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_strain: S2 Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmtbip
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.096 87.205 124.274 90.00 94.31 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand NAG enzyme
note 3BT2 is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
A


B


U


Primary referenceCrystal structures of two human vitronectin, urokinase and urokinase receptor complexes., Huai Q, Zhou A, Lin L, Mazar AP, Parry GC, Callahan J, Shaw DE, Furie B, Furie BC, Huang M, Nat Struct Mol Biol. 2008 Apr;15(4):422-3. Epub 2008 Mar 23. PMID:18376415
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (141 Kb) [Save to disk]
  • Biological Unit Coordinates (3bt2.pdb1.gz) 133 Kb
  • Biological Unit Coordinates (3bt2.pdb2.gz) 126 Kb
  • Biological Unit Coordinates (3bt2.pdb3.gz) 10 Kb
  • LPC: Ligand-Protein Contacts for 3BT2
  • CSU: Contacts of Structural Units for 3BT2
  • Likely Quarternary Molecular Structure file(s) for 3BT2
  • Structure Factors (569 Kb)
  • Retrieve 3BT2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BT2 from S2C, [Save to disk]
  • Re-refined 3bt2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BT2 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 3BT2
  • 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 3BT2, from MSDmotif at EBI
  • Fold representative 3bt2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bt2] [3bt2_H] [3bt2_B] [3bt2_A] [3bt2_U] [3bt2_L]
  • SWISS-PROT database: [P01837] [P01675] [Q03405] [P00749] [P04004]
  • Domain organization of [IGKC_MOUSE] [KV6A1_MOUSE] [UPAR_HUMAN] [UROK_HUMAN] [VTNC_HUMAN] by SWISSPFAM
  • Domains found in 3BT2: [EGF] [IG_like] [IGv] [KR] [LU] [SO ] by SMART
  • Other resources with information on 3BT2
  • Community annotation for 3BT2 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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