1VI9 Crystal structure of pyridoxamine kinase date
authors GenomiX, Structural.
compound source
symmetry
R_factor
R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.96
ligand BME, CSD, MSE, SO4 enzyme
related structures by homologous chain: 1TD2
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural analysis of a set of proteins resulting from a bacterial genomics project., Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ, Proteins 2005 Sep 1;60(4):787-96. PMID:16021622
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (205 Kb) [Save to disk]
  • Biological Unit Coordinates (1vi9.pdb1.gz) 101 Kb
  • Biological Unit Coordinates (1vi9.pdb2.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 1VI9
  • CSU: Contacts of Structural Units for 1VI9
  • Likely Quarternary Molecular Structure file(s) for 1VI9
  • Structure Factors (1866 Kb)
  • Retrieve 1VI9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VI9 from S2C, [Save to disk]
  • Re-refined 1vi9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VI9 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 1VI9
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1VI9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vi9a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vi9b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1vi9c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1vi9d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1vi9 from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1vi9_A] [1vi9_B] [1vi9_D] [1vi9] [1vi9_C]
  • SWISS-PROT database: [P77150]
  • Domain organization of [PDXY_ECOLI] by SWISSPFAM
    • Other resources with information on 1VI9
  • Community annotation for 1VI9 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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