1S3R Toxin date Jan 14, 2004
title Crystal Structure Of The Human-Specific Toxin Intermedilysin
authors G.Polekhina, K.S.Giddings, R.K.Tweten, M.W.Parker
compound source
Molecule: Intermedilysin
Chain: A, B
Engineered: Yes
 Organism_scientific: Streptococcus Intermedius
Organism_taxid: 1338
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrchisa
symmetry Space Group: P 21 21 2
R_factor 0.229 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
88.450 173.640 105.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • toxin activity


    • Primary referenceInsights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin., Polekhina G, Giddings KS, Tweten RK, Parker MW, Proc Natl Acad Sci U S A 2005 Jan 18;102(3):600-5. Epub 2005 Jan 06. PMID:15637162
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (161 Kb) [Save to disk]
  • Biological Unit Coordinates (1s3r.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (1s3r.pdb2.gz) 79 Kb
  • Biological Unit Coordinates (1s3r.pdb3.gz) 154 Kb
  • Biological Unit Coordinates (1s3r.pdb4.gz) 305 Kb
  • LPC: Ligand-Protein Contacts for 1S3R
  • CSU: Contacts of Structural Units for 1S3R
  • Likely Quarternary Molecular Structure file(s) for 1S3R
  • Structure Factors (365 Kb)
  • Retrieve 1S3R in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S3R from S2C, [Save to disk]
  • Re-refined 1s3r structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1S3R 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 1S3R
  • 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 1S3R, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s3r_A] [1s3r] [1s3r_B]
  • SWISS-PROT database: [Q9LCB8]
  • Belongs to the thiol-activated cholesterol-dependent cytolysin (cdc) family according to TCDB.
  • Domain organization of [Q9LCB8_STRIT] by SWISSPFAM
    • Other resources with information on 1S3R
  • Community annotation for 1S3R 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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