1VK0 Structural Genomics, Unknown Function date Apr 12, 2004
title X-Ray Structure Of Gene Product From Arabidopsis Thaliana At
authors G.E.Wesenberg, D.W.Smith, G.N.Phillips Jr., K.A.Johnson, C.A.Bin Center For Eukaryotic Structural Genomics (Cesg)
compound source
Molecule: Hypothetical Protein
Chain: A, B, C, D, E, F
Engineered: Yes
 Organism_scientific: Arabidopsis Thaliana
Organism_common: Thale Cress
Organism_taxid: 3702
Gene: At5g06450
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 32 2 1
R_factor 0.180 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
120.831 120.831 185.222 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand MSE enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B
  • nuclease activity
  • single-stranded DNA 3'-5' ex...
  • 3'-5' exonuclease activity
  • exoribonuclease II activity


    • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (207 Kb) [Save to disk]
  • Biological Unit Coordinates (1vk0.pdb1.gz) 202 Kb
  • LPC: Ligand-Protein Contacts for 1VK0
  • CSU: Contacts of Structural Units for 1VK0
  • Likely Quarternary Molecular Structure file(s) for 1VK0
  • Structure Factors (5163 Kb)
  • Retrieve 1VK0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VK0 from S2C, [Save to disk]
  • Re-refined 1vk0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VK0 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 1VK0
  • 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 1VK0, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vk0a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vk0b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1vk0c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1vk0d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1vk0e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1vk0f_, region F [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vk0_D] [1vk0_B] [1vk0] [1vk0_F] [1vk0_A] [1vk0_E] [1vk0_C]
  • SWISS-PROT database: [Q9FNG3]
  • Domain organization of [Y5645_ARATH] by SWISSPFAM
    • Other resources with information on 1VK0
  • Community annotation for 1VK0 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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