1YEF Catalytic Antibody date May 29, 1997
title Structure Of Igg2a Fab Fragment (D2.3) Complexed With Substr Analogue
authors B.Gigant, M.Knossow
compound source
Molecule: Igg2a Fab Fragment
Chain: L
Other_details: Structure Of Igg2a Fab Fragment (D2.3)
 Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Igg2a Fab Fragment
Chain: H
Other_details: Structure Of Igg2a Fab Fragment (D2.3)
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
symmetry Space Group: P 31 2 1
R_factor 0.199 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.200 78.200 158.700 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand PNC, ZN enzyme
related structures by homologous chain: 1HIL, 1UYW, 1YEG
Primary referenceX-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release., Gigant B, Charbonnier JB, Eshhar Z, Green BS, Knossow M, Proc Natl Acad Sci U S A 1997 Jul 22;94(15):7857-61. PMID:9223277
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (1yef.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 1YEF
  • CSU: Contacts of Structural Units for 1YEF
  • Likely Quarternary Molecular Structure file(s) for 1YEF
  • Retrieve 1YEF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YEF from S2C, [Save to disk]
    • View 1YEF 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 1YEF
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1YEF, from MSDmotif at EBI
  • Genome occurence of 1YEF's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1yefh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1yefh2, region H:114-223 [Jmol] [rasmolscript] [script source]
        - Domain d1yefl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1yefl2, region L:108-214 [Jmol] [rasmolscript] [script source]
  • 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: [1yef] [1yef_H] [1yef_L]
  • SWISS-PROT database: [P01863]
  • Domain organization of [GCAA_MOUSE] by SWISSPFAM
  • Domains found in 1YEF: [IG_like] [IGv ] by SMART
    • Other resources with information on 1YEF
  • Community annotation for 1YEF 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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