1F3F STRUCTURE OF THE H122G NUCLEOSIDE DIPHOSPHATE KINASE / D4T-TRIPHOSPHATE.MG COMPLEX date
authors Meyer, P., Schneider, B., Sarfati, S., Deville-Bonne, D., Guerreiro, C., Boretto, J., Janin, J., Veron, M., Canard, B.
compound source
symmetry
R_factor
R_Free 0.2340000
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.85
ligand D4D, D4T, MG, PO4 enzyme
related structures by homologous chain: 1HLW, 1NPK
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructural basis for activation of alpha-boranophosphate nucleotide analogues targeting drug-resistant reverse transcriptase., Meyer P, Schneider B, Sarfati S, Deville-Bonne D, Guerreiro C, Boretto J, Janin J, Veron M, Canard B, EMBO J 2000 Jul 17;19(14):3520-9. PMID:10899107
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (1f3f.pdb1.gz) 152 Kb
  • LPC: Ligand-Protein Contacts for 1F3F
  • CSU: Contacts of Structural Units for 1F3F
  • Likely Quarternary Molecular Structure file(s) for 1F3F
  • Retrieve 1F3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1F3F from S2C, [Save to disk]
    • View 1F3F 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 1F3F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1F3F, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1f3fa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1f3fb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1f3fc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1f3f 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: [1f3f] [1f3f_A] [1f3f_C] [1f3f_B]
  • SWISS-PROT database: [P22887]
  • Domain organization of [NDKC_DICDI] by SWISSPFAM
  • Domain found in 1F3F: [NDK ] by SMART
    • Other resources with information on 1F3F
  • Community annotation for 1F3F 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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