4YO0 Crystal structure of monoclonal anti-human podoplanin antibody NZ-1 with bound PA peptide date
authors Fujii, Y., Kitago, Y., Arimori, T., Takagi, J.
compound source
symmetry
R_factor
R_Free 0.2141
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.56
ligand EDO, PCA enzyme
Primary referenceTailored placement of a turn-forming PA tag into the structured domain of a protein to probe its conformational state., Fujii Y, Matsunaga Y, Arimori T, Kitago Y, Ogasawara S, Kaneko MK, Kato Y, Takagi J, J Cell Sci. 2016 Feb 12. pii: jcs.176685. PMID:26872787
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (289 Kb) [Save to disk]
  • Biological Unit Coordinates (4yo0.pdb1.gz) 145 Kb
  • Biological Unit Coordinates (4yo0.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 4YO0
  • CSU: Contacts of Structural Units for 4YO0
  • Structure Factors (1072 Kb)
  • Retrieve 4YO0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4YO0 from S2C, [Save to disk]
  • Re-refined 4yo0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4YO0 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 4YO0
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4yo0_C] [4yo0_E] [4yo0_B] [4yo0] [4yo0_A] [4yo0_F] [4yo0_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4YO0: [IG_like] [IGv ] by SMART
    • Other resources with information on 4YO0
  • Community annotation for 4YO0 at PDBWiki (http://pdbwiki.org)

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