1S5D Transferase,Toxin date Jan 20, 2004
title Cholera Holotoxin With An A-Subunit Y30s Mutation, Crystal F
authors C.J.O'Neal, E.I.Amaya, M.G.Jobling, R.K.Holmes, W.G.Hol
compound source
Molecule: Cholera Enterotoxin, A Chain
Chain: A
Synonym: Nad(+)--Diphthamide Adp- Ribosyltransferase, Chole Enterotoxin A Subunit;
Ec: 2.4.2.36
Engineered: Yes
Mutation: Yes
 Organism_scientific: Vibrio Cholerae
Organism_taxid: 666
Gene: Ctxa, Toxa, Vc1457
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Peia154

Molecule: Cholera Toxin B Protein (Ctb)
Chain: D, E, F, G, H
Engineered: Yes
Organism_scientific: Vibrio Cholerae
Organism_taxid: 666
Gene: Ctxb, Toxb, Vc1456
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Peia154
symmetry Space Group: P 21 21 21
R_factor 0.161 R_Free 0.191
crystal
cell
length a length b length c angle alpha angle beta angle gamma
60.055 111.904 124.656 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand GAL, GOL, NA enzyme Transferase E.C.2.4.2.36 BRENDA
note 1S5D is a representative structure
related structures by homologous chain: 1EEF, 1LT5, 1S5E
Gene
Ontology
ChainFunctionProcessComponent
A
  • toxin activity


    • H, F, D, G, E
  • host cell surface binding
  • toxin activity


    • Primary referenceCrystal Structures of an Intrinsically Active Cholera Toxin Mutant Yield Insight into the Toxin Activation Mechanism(,)., O'Neal CJ, Amaya EI, Jobling MG, Holmes RK, Hol WG, Biochemistry 2004 Apr 6;43(13):3772-3782. PMID:15049684
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (1s5d.pdb1.gz) 125 Kb
  • LPC: Ligand-Protein Contacts for 1S5D
  • CSU: Contacts of Structural Units for 1S5D
  • Likely Quarternary Molecular Structure file(s) for 1S5D
  • Structure Factors (1339 Kb)
  • Retrieve 1S5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S5D from S2C, [Save to disk]
  • Re-refined 1s5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1S5D 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 1S5D
  • 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 1S5D, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s5da_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1s5dd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1s5de_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1s5df_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1s5dg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1s5dh_, region H [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: [1s5d_H] [1s5d_D] [1s5d] [1s5d_G] [1s5d_A] [1s5d_E] [1s5d_F]
  • SWISS-PROT database: [P01555] [P01556]
  • Domain organization of [CHTA_VIBCH] [CHTB_VIBCH] by SWISSPFAM
    • Other resources with information on 1S5D
  • Community annotation for 1S5D 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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