1QD2 Hydrolase date Jul 09, 1999
title Crystal Structure Of The Complex Of Trichosanthin With Adeni Obtained From Trichosanthin Complexed With The Dinucleotide
authors Y.J.Gu, Z.X.Xia
compound source
Molecule: Trichosanthin
Chain: A
Synonym: Ribosome-Inactivating Protein Alpha-Trichosanthin, Glycosidase, Alpha-Tcs;
Ec: 3.2.2.22
 Organism_scientific: Trichosanthes Kirilowii
Organism_taxid: 3677
symmetry Space Group: P 21 21 21
R_factor 0.163 R_Free 0.221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.410 76.720 79.450 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.86 Å
ligand ADE enzyme Hydrolase E.C.3.2.2.22 BRENDA
related structures by homologous chain: 1GIU, 1NLI
Gene
Ontology
ChainFunctionProcessComponent
A
  • toxin activity


    • Primary referenceCrystal structures of the complexes of trichosanthin with four substrate analogs and catalytic mechanism of RNA N-glycosidase., Gu YJ, Xia ZX, Proteins 2000 Apr 1;39(1):37-46. PMID:10737925
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (46 Kb) [Save to disk]
  • Biological Unit Coordinates (1qd2.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 1QD2
  • CSU: Contacts of Structural Units for 1QD2
  • Likely Quarternary Molecular Structure file(s) for 1QD2
  • Structure Factors (163 Kb)
  • Retrieve 1QD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QD2 from S2C, [Save to disk]
  • Re-refined 1qd2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1QD2 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 1QD2
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1QD2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qd2a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1g1qd2, region D:119-160 [Jmol] [rasmolscript] [script source]
        - Domain d1h1qd2, region D:310-432 [Jmol] [rasmolscript] [script source]
        - Domain d1e1qd2, region D:9-81 [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: [1qd2] [1qd2_A]
  • SWISS-PROT database: [P09989]
  • Domain organization of [RIPT_TRIKI] by SWISSPFAM
    • Other resources with information on 1QD2
  • Community annotation for 1QD2 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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