3KYM Crystal structure of Li33 IgG2 di-Fab date
authors Silvian, L.F., Pepinsky, R.B., Walus, L.
compound source
symmetry
R_factor
R_Free 0.33904
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.62
Primary referenceImproving the solubility of anti-LINGO-1 monoclonal antibody Li33 by isotype switching and targeted mutagenesis., Pepinsky RB, Silvian L, Berkowitz SA, Farrington G, Lugovskoy A, Walus L, Eldredge J, Capili A, Mi S, Graff C, Garber E, Protein Sci. 2010 Mar 2. PMID:20198683
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (536 Kb) [Save to disk]
  • Biological Unit Coordinates (3kym.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (3kym.pdb2.gz) 75 Kb
  • Biological Unit Coordinates (3kym.pdb3.gz) 75 Kb
  • Biological Unit Coordinates (3kym.pdb4.gz) 75 Kb
  • Biological Unit Coordinates (3kym.pdb5.gz) 75 Kb
  • Biological Unit Coordinates (3kym.pdb6.gz) 74 Kb
  • Biological Unit Coordinates (3kym.pdb7.gz) 75 Kb
  • Biological Unit Coordinates (3kym.pdb8.gz) 75 Kb
  • CSU: Contacts of Structural Units for 3KYM
  • Structure Factors (1859 Kb)
  • Retrieve 3KYM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KYM from S2C, [Save to disk]
  • Re-refined 3kym structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3KYM 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 3KYM
  • 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 3KYM, from MSDmotif at EBI
  • Fold representative 3kym from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kym_E] [3kym_A] [3kym_J] [3kym_P] [3kym_B] [3kym_F] [3kym] [3kym_D] [3kym_I] [3kym_L] [3kym_K] [3kym_H] [3kym_M] [3kym_C] [3kym_G] [3kym_O] [3kym_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KYM: [IG_like] [IGv ] by SMART
    • Other resources with information on 3KYM
  • Community annotation for 3KYM 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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