1VKM Crystal structure of an indigoidine synthase a (idga)-like protein (tm1464) from thermotoga maritima msb8 at 1.90 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.19959
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.90
ligand EDO, MN, MSE, UNL enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • pseudouridylate synthase act...


    • Primary referenceCrystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold., Levin I, Miller MD, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Morse A, Moy K, Nigoghossian E, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, Wilson IA, Proteins 2005 Jun 1;59(4):864-8. PMID:15822122
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (309 Kb) [Save to disk]
  • Biological Unit Coordinates (1vkm.pdb1.gz) 150 Kb
  • Biological Unit Coordinates (1vkm.pdb2.gz) 150 Kb
  • Biological Unit Coordinates (1vkm.pdb3.gz) 293 Kb
  • LPC: Ligand-Protein Contacts for 1VKM
  • CSU: Contacts of Structural Units for 1VKM
  • Likely Quarternary Molecular Structure file(s) for 1VKM
  • Structure Factors (20240 Kb)
  • Retrieve 1VKM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VKM from S2C, [Save to disk]
  • Re-refined 1vkm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VKM 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 1VKM
  • 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 1VKM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vkma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vkmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1vkmc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1vkmd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1vkme_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1vkmf_, region F [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vkm_B] [1vkm_E] [1vkm_F] [1vkm] [1vkm_D] [1vkm_A] [1vkm_C]
  • SWISS-PROT database: [Q9X1H5]
  • Domain organization of [PSUG_THEMA] by SWISSPFAM
    • Other resources with information on 1VKM
  • Community annotation for 1VKM 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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