1KEG Antibody 64M-2 Fab complexed with dTT(6-4)TT date
authors Yokoyama, H., Mizutani, R., Satow, Y., Sato, K., Komatsu, Y., Ohtsuka, E., Nikaido, O.
compound source
symmetry
R_factor
R_Free 0.268
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand 64T, NI enzyme
related structures by homologous chain: 1AP2, 1C5D, 1NGP, 1R3I
Primary referenceStructure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides., Yokoyama H, Mizutani R, Satow Y, Sato K, Komatsu Y, Ohtsuka E, Nikaido O, Acta Crystallogr D Biol Crystallogr. 2012 Mar;68(Pt 3):232-8. Epub 2012 Feb 7. PMID:22349224
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (1keg.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 1KEG
  • CSU: Contacts of Structural Units for 1KEG
  • Likely Quarternary Molecular Structure file(s) for 1KEG
  • Structure Factors (158 Kb)
  • Retrieve 1KEG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KEG from S2C, [Save to disk]
  • Re-refined 1keg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KEG 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 1KEG
  • 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 1KEG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kegh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1kegh2, region H:114-228 [Jmol] [rasmolscript] [script source]
        - Domain d1kegl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1kegl2, region L:108-212 [Jmol] [rasmolscript] [script source]
  • Fold representative 1keg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1keg] [1keg_A] [1keg_L] [1keg_H]
  • SWISS-PROT database: [P01863]
  • Domain organization of [GCAA_MOUSE] by SWISSPFAM
  • Domains found in 1KEG: [IG_like] [IGv ] by SMART
  • Other resources with information on 1KEG
  • Community annotation for 1KEG 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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