5GIR Immune System date Jun 24, 2016
title Crystal Structure Of A Fab Fragment With Its Ligand Peptide
authors Y.Kitago, K.K.Kaneko, S.Ogasawara, Y.Kato, J.Takagi
compound source
Molecule: Heavy Chain Of Fab Fragment
Chain: H, A
Engineered: Yes
 Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mammalia
Expression_system_taxid: 40674
Expression_system_cell: Hybridoma

Molecule: Light Chain Of Fab Fragment
Chain: L, B
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Mammalia
Expression_system_taxid: 40674
Expression_system_cell: Hybridoma

Molecule: Lys-Pro-Ile-Ile-Ile-Gly-Ser-His-Ala-Tyr-Gly-Asp
Chain: C, D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.182 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
69.110 93.650 70.560 90.00 107.51 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand EDO, PCA, SO4 enzyme
Primary referenceStructural basis for multi-specific peptide recognition by the anti-IDH1/2 monoclonal antibody, MsMab-1., Kitago Y, Kaneko MK, Ogasawara S, Kato Y, Takagi J, Biochem Biophys Res Commun. 2016 Sep 23;478(3):1274-9. doi:, 10.1016/j.bbrc.2016.08.110. Epub 2016 Aug 20. PMID:27553275
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (5gir.pdb1.gz) 140 Kb
  • Biological Unit Coordinates (5gir.pdb2.gz) 140 Kb
  • LPC: Ligand-Protein Contacts for 5GIR
  • CSU: Contacts of Structural Units for 5GIR
  • Structure Factors (572 Kb)
  • Retrieve 5GIR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5GIR from S2C, [Save to disk]
  • Re-refined 5gir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5GIR 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 5GIR
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5gir_L] [5gir_C] [5gir_H] [5gir_B] [5gir_D] [5gir] [5gir_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5GIR: [IG_like] [IGv ] by SMART
    • Other resources with information on 5GIR
  • Community annotation for 5GIR at PDBWiki (http://pdbwiki.org)

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