1VK3 Crystal structure of Phosphoribosylformylglycinamidine synthase II (TM1246) from Thermotoga maritima at 2.15 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.25423
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.15
ligand CL, MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution., Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Wilson IA, Proteins. 2006 Jun 1;63(4):1106-11. PMID:16544324
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (1vk3.pdb1.gz) 93 Kb
  • LPC: Ligand-Protein Contacts for 1VK3
  • CSU: Contacts of Structural Units for 1VK3
  • Likely Quarternary Molecular Structure file(s) for 1VK3
  • Structure Factors (2226 Kb)
  • Retrieve 1VK3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VK3 from S2C, [Save to disk]
  • Re-refined 1vk3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VK3 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 1VK3
  • 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 1VK3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vk3a3, region A:167-345 [Jmol] [rasmolscript] [script source]
        - Domain d1vk3a1, region A:2-166 [Jmol] [rasmolscript] [script source]
        - Domain d1vk3a2, region A:346-507 [Jmol] [rasmolscript] [script source]
        - Domain d1vk3a4, region A:508-603 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vk3] [1vk3_A]
  • SWISS-PROT database: [Q9X0X3]
  • Domain organization of [PURL_THEMA] by SWISSPFAM
    • Other resources with information on 1VK3
  • Community annotation for 1VK3 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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