4DVB The crystal structure of the Fab fragment of pro-uPA antibody mAb-112 date
authors Jiang, L., Botkjaer, K.A., Andersen, L.M., Yuan, C., Andreasen, P.A., Huang, M.
compound source
symmetry
R_factor
R_Free 0.25899
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.93
ligand PG4, SO4 enzyme
Primary referenceRezymogenation of active urokinase induced by an inhibitory antibody., Jiang L, Botkjaer KA, Andersen LM, Yuan C, Andreasen PA, Huang M, Biochem J. 2013 Jan 1;449(1):161-6. doi: 10.1042/BJ20121132. PMID:23016918
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (4dvb.pdb1.gz) 73 Kb
  • Biological Unit Coordinates (4dvb.pdb2.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 4DVB
  • CSU: Contacts of Structural Units for 4DVB
  • Structure Factors (879 Kb)
  • Retrieve 4DVB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DVB from S2C, [Save to disk]
  • Re-refined 4dvb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DVB 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 4DVB
  • 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
  • 3D motif for 4DVB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dvb_H] [4dvb_L] [4dvb_A] [4dvb_B] [4dvb]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DVB: [IG_like] [IGv ] by SMART
    • Other resources with information on 4DVB
  • Community annotation for 4DVB at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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