2DDB Toxin date Jan 25, 2006
title Crystal Structure Of Pseudecin From Pseudechis Porphyriacus
authors N.Suzuki, Y.Yamazaki, Z.Fujimoto, T.Morita, H.Mizuno
compound source
Molecule: Pseudecin
Chain: A, B, C, D
Synonym: Channel Blocker
 Organism_scientific: Pseudechis Porphyriacus
Organism_common: Red-Bellied Black Snake
Organism_taxid: 8671
Tissue: Venom
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.707 61.668 251.224 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand FMT, GOL, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • toxin activity


    • Primary referenceStructures of pseudechetoxin and pseudecin, two snake-venom cysteine-rich secretory proteins that target cyclic nucleotide-gated ion channels: implications for movement of the C-terminal cysteine-rich domain., Suzuki N, Yamazaki Y, Brown RL, Fujimoto Z, Morita T, Mizuno H, Acta Crystallogr D Biol Crystallogr. 2008 Oct;64(Pt 10):1034-42. Epub 2008, Sep 19. PMID:18931410
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (2ddb.pdb1.gz) 40 Kb
  • Biological Unit Coordinates (2ddb.pdb2.gz) 40 Kb
  • Biological Unit Coordinates (2ddb.pdb3.gz) 40 Kb
  • Biological Unit Coordinates (2ddb.pdb4.gz) 39 Kb
  • LPC: Ligand-Protein Contacts for 2DDB
  • CSU: Contacts of Structural Units for 2DDB
  • Likely Quarternary Molecular Structure file(s) for 2DDB
  • Structure Factors (1125 Kb)
  • Retrieve 2DDB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2DDB from S2C, [Save to disk]
  • Re-refined 2ddb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2DDB 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 2DDB
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2DDB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ddb] [2ddb_B] [2ddb_C] [2ddb_D] [2ddb_A]
  • SWISS-PROT database: [Q8AVA3]
  • Domain organization of [CRVP_PSEPO] by SWISSPFAM
  • Domain found in 2DDB: [SCP ] by SMART
    • Other resources with information on 2DDB
  • Community annotation for 2DDB 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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