1LY0 Plant Protein date Jun 06, 2002
title Structure Of Thaumatin Crystallized In The Presence Of Glycerol
authors C.Charron, A.Kadri, M.C.Robert, R.Giege, B.Lorber
compound source
Molecule: Thaumatin I
Chain: A
 Organism_scientific: Thaumatococcus Daniellii
Organism_common: Miracle Fruit
Organism_taxid: 4621
symmetry Space Group: P 41 21 2
R_factor 0.195 R_Free 0.204
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.867 57.867 149.960 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.36 Å
ligand TLA enzyme
related structures by homologous chain: 1LXZ, 1PP3
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystallization in the presence of glycerol displaces water molecules in the structure of thaumatin., Charron C, Kadri A, Robert MC, Giege R, Lorber B, Acta Crystallogr D Biol Crystallogr 2002 Dec;58(Pt 12):2060-5. PMID:12454465
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (1ly0.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 1LY0
  • CSU: Contacts of Structural Units for 1LY0
  • Likely Quarternary Molecular Structure file(s) for 1LY0
  • Structure Factors (379 Kb)
  • Retrieve 1LY0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LY0 from S2C, [Save to disk]
  • Re-refined 1ly0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1LY0 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 1LY0
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Conformational Epitope Prediction for 1LY0 from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1LY0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ly0a_, region A [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: [1ly0] [1ly0_A]
  • SWISS-PROT database: [P02883]
  • Domain organization of [THM1_THADA] by SWISSPFAM
  • Domain found in 1LY0: [THN ] by SMART
    • Other resources with information on 1LY0
  • Community annotation for 1LY0 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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