1VK8 CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.18956
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.80
ligand MSE, UNL enzyme
Primary referenceTM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions., Dermoun Z, Foulon A, Miller MD, Harrington DJ, Deacon AM, Sebban-Kreuzer C, Roche P, Lafitte D, Bornet O, Wilson IA, Dolla A, J Mol Biol. 2010 Jul 16;400(3):463-76. Epub 2010 May 13. PMID:20471400
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (1vk8.pdb1.gz) 68 Kb
  • LPC: Ligand-Protein Contacts for 1VK8
  • CSU: Contacts of Structural Units for 1VK8
  • Likely Quarternary Molecular Structure file(s) for 1VK8
  • Structure Factors (1923 Kb)
  • Retrieve 1VK8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VK8 from S2C, [Save to disk]
  • Re-refined 1vk8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VK8 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 1VK8
  • 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 1VK8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vk8a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vk8b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1vk8c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1vk8d_, region D [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vk8_D] [1vk8_A] [1vk8_B] [1vk8_C] [1vk8]
  • SWISS-PROT database: [Q9WYV6]
  • Domain organization of [Q9WYV6_THEMA] by SWISSPFAM
    • Other resources with information on 1VK8
  • Community annotation for 1VK8 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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