1YED Catalytic Antibody date Apr 15, 1997
title Structure Of A Catalytic Antibody Igg2a Fab Fragment (D2.4)
authors B.Golinelli-Pimpaneau, M.Knossow
compound source
Molecule: Igg1 Fab Fragment (D.2.4)
Chain: L, A
Other_details: Transition State Analogue
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090

Molecule: Igg1 Fab Fragment (D.2.4)
Chain: H, B
Other_details: Transition State Analogue

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
symmetry Space Group: C 2 2 21
R_factor 0.215 R_Free 0.260
length a length b length c angle alpha angle beta angle gamma
99.250 104.790 223.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand PNB enzyme
Primary referenceStructural convergence in the active sites of a family of catalytic antibodies., Charbonnier JB, Golinelli-Pimpaneau B, Gigant B, Tawfik DS, Chap R, Schindler DG, Kim SH, Green BS, Eshhar Z, Knossow M, Science 1997 Feb 21;275(5303):1140-2. PMID:9027317
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (134 Kb) [Save to disk]
  • Biological Unit Coordinates (1yed.pdb1.gz) 66 Kb
  • Biological Unit Coordinates (1yed.pdb2.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 1YED
  • CSU: Contacts of Structural Units for 1YED
  • Likely Quarternary Molecular Structure file(s) for 1YED
  • Retrieve 1YED in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YED from S2C, [Save to disk]
  • View 1YED 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 1YED
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1YED, from MSDmotif at EBI
  • Genome occurence of 1YED's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1yeda1, region A:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1yeda2, region A:111-222 [Jmol] [rasmolscript] [script source]
        - Domain d1yedb1, region B:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1yedb2, region B:116-217 [Jmol] [rasmolscript] [script source]
        - Domain d1yedh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1yedh2, region H:116-217 [Jmol] [rasmolscript] [script source]
        - Domain d1yedl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1yedl2, region L:111-222 [Jmol] [rasmolscript] [script source]
  • Fold representative 1yed 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: [1yed_L] [1yed_B] [1yed_H] [1yed] [1yed_A]
  • SWISS-PROT database: [P01868]
  • Domain organization of [IGHG1_MOUSE] by SWISSPFAM
  • Domains found in 1YED: [IG_like] [IGv ] by SMART
  • Other resources with information on 1YED
  • Community annotation for 1YED at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1YED from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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