1RFV Crystal structure of pyridoxal kinase complexed with ADP date
authors Liang, D.C., Jiang, T., Li, M.H.
compound source
symmetry
R_factor
R_Free 0.222
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand ADP, ZN enzyme
related structures by homologous chain: 1LHR, 1RFT
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (1rfv.pdb1.gz) 101 Kb
  • LPC: Ligand-Protein Contacts for 1RFV
  • CSU: Contacts of Structural Units for 1RFV
  • Likely Quarternary Molecular Structure file(s) for 1RFV
  • Structure Factors (251 Kb)
  • Retrieve 1RFV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RFV from S2C, [Save to disk]
  • Re-refined 1rfv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RFV 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 1RFV
  • 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 1RFV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rfva_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1rfvb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1rfv from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1rfv_B] [1rfv_A] [1rfv]
  • SWISS-PROT database: [P82197]
  • Domain organization of [PDXK_SHEEP] by SWISSPFAM
  • Other resources with information on 1RFV
  • Community annotation for 1RFV 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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