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
crystal cell	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 Diffraction	resolution	3.10 Å
ligand	PNB	enzyme
Primary reference	Structural 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] (132 Kb) [Save to disk] Biological Unit Coordinates (1yed.pdb1.gz) 65 Kb Biological Unit Coordinates (1yed.pdb2.gz) 65 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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server 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] 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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