1SKS Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template date
authors Li, Y., Dutta, S., Doublie, S., Bdour, H.M., Taylor, J.S., Ellenberger, T.
compound source
symmetry
R_factor
R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.30
ligand 2DT, MG, TTD enzyme
related structures by homologous chain: 1SKW, 1X9W
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


    • B
  • DNA polymerase processivity ...


    • Primary referenceNucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7., Li Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T, Nat Struct Mol Biol 2004 Aug;11(8):784-90. Epub 2004 Jul 4. PMID:15235589
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (1sks.pdb1.gz) 138 Kb
  • LPC: Ligand-Protein Contacts for 1SKS
  • CSU: Contacts of Structural Units for 1SKS
  • Likely Quarternary Molecular Structure file(s) for 1SKS
  • Structure Factors (439 Kb)
  • Retrieve 1SKS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SKS from S2C, [Save to disk]
  • Re-refined 1sks structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1SKS 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 1SKS
  • 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 1SKS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sksa1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1sksa2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1sksb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1sks 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: [1sks_T] [1sks_P] [1sks_A] [1sks] [1sks_B]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1SKS: [POLAc ] by SMART
    • Other resources with information on 1SKS
  • Community annotation for 1SKS 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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