2FD6 Immune System, Hydrolase date Dec 13, 2005
title Structure Of Human Urokinase Plasminogen Activator In Comple Urokinase Receptor And An Anti-Upar Antibody At 1.9 A
authors M.Huang, Q.Huai, Y.Li
compound source
Molecule: Urokinase-Type Plasminogen Activator
Chain: A
Fragment: Amino Terminal Residues 31-152
Ec: 3.4.21.73
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila
Expression_system_common: Fruit Flies
Expression_system_taxid: 7215
Expression_system_cell_line: S2 Cells
Expression_system_vector: Pmt-Bip-V5-His

Molecule: L Chain Of Fab Of Atn-615 Anti-Upar Antibody
Chain: L

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Secretion: Ascite Liquid

Molecule: H Chain Of Fab Of Atn-615 Anti-Upar Antibody
Chain: H

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Secretion: Ascite Liquid

Molecule: Urokinase Plasminogen Activator Surface Receptor
Chain: U
Fragment: Residues 23-297
Synonym: Upar, U-Par, Monocyte Activation Antigen Mo3, Cd87
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Drosophila
Expression_system_common: Fruit Flies
Expression_system_taxid: 7215
Expression_system_cell_line: S2 Cells
Expression_system_vector: Pmt-Bip-V5-His
symmetry Space Group: P 1 21 1
R_factor 0.239 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.792 86.805 124.690 90.00 94.54 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand EDO, ETX, FUC, NAG, NDG, PG4, PGE, SO4 enzyme Hydrolase E.C.3.4.21.73 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


L


U


Primary referenceStructure of human urokinase plasminogen activator in complex with its receptor., Huai Q, Mazar AP, Kuo A, Parry GC, Shaw DE, Callahan J, Li Y, Yuan C, Bian C, Chen L, Furie B, Furie BC, Cines DB, Huang M, Science. 2006 Feb 3;311(5761):656-9. PMID:16456079
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (2fd6.pdb1.gz) 133 Kb
  • Biological Unit Coordinates (2fd6.pdb2.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 2FD6
  • CSU: Contacts of Structural Units for 2FD6
  • Likely Quarternary Molecular Structure file(s) for 2FD6
  • Structure Factors (631 Kb)
  • Retrieve 2FD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FD6 from S2C, [Save to disk]
  • Re-refined 2fd6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2FD6 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 2FD6
  • 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 2FD6, from MSDmotif at EBI
  • Fold representative 2fd6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2fd6_U] [2fd6_A] [2fd6_H] [2fd6_L] [2fd6]
  • SWISS-PROT database: [Q52L64] [Q924Q0] [Q03405] [P00749]
  • Domain organization of [Q52L64_MOUSE] [Q924Q0_MOUSE] [UPAR_HUMAN] [UROK_HUMAN] by SWISSPFAM
  • Domains found in 2FD6: [IG_like] [IGv] [KR] [LU ] by SMART
  • Other resources with information on 2FD6
  • Community annotation for 2FD6 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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