1RFU Crystal structure of pyridoxal kinase complexed with ADP and PLP date
authors Liang, D.C., Jiang, T., Li, M.H.
compound source
symmetry
R_factor
R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand ADP, PLP, ZN enzyme
related structures by homologous chain: 1RFT
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceConformational changes in the reaction of pyridoxal kinase., Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T, Liang DC, J Biol Chem 2004 Apr 23;279(17):17459-65. Epub 2004 Jan 13. PMID:14722069
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (413 Kb) [Save to disk]
  • Biological Unit Coordinates (1rfu.pdb1.gz) 107 Kb
  • Biological Unit Coordinates (1rfu.pdb2.gz) 106 Kb
  • Biological Unit Coordinates (1rfu.pdb3.gz) 105 Kb
  • Biological Unit Coordinates (1rfu.pdb4.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 1RFU
  • CSU: Contacts of Structural Units for 1RFU
  • Likely Quarternary Molecular Structure file(s) for 1RFU
  • Structure Factors (946 Kb)
  • Retrieve 1RFU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RFU from S2C, [Save to disk]
    • View 1RFU 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 1RFU
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RFU, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rfua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rfub_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1rfuc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1rfud_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1rfue_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1rfuf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1rfug_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1rfuh_, region H [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1rfu_G] [1rfu_A] [1rfu_B] [1rfu_F] [1rfu] [1rfu_D] [1rfu_C] [1rfu_E] [1rfu_H]
  • SWISS-PROT database: [P82197]
  • Domain organization of [PDXK_SHEEP] by SWISSPFAM
    • Other resources with information on 1RFU
  • Community annotation for 1RFU 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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