1X9W T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide. date
authors Dutta, S., Li, Y., Johnson, D., Dzantiev, L., Richardson, C.C., Romano, L.J., Ellenberger, T.
compound source
symmetry
R_factor
R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.30
ligand 2DT, MG enzyme
related structures by homologous chain: 1SKS, 1TK0
Gene
Ontology
ChainFunctionProcessComponent
A
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • B
  • DNA polymerase processivity ...


  • Primary referenceCrystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis., Dutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T, Proc Natl Acad Sci U S A 2004 Nov 16;101(46):16186-91. Epub . PMID:15528277
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]
  • Biological Unit Coordinates (1x9w.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 1X9W
  • CSU: Contacts of Structural Units for 1X9W
  • Likely Quarternary Molecular Structure file(s) for 1X9W
  • Structure Factors (437 Kb)
  • Retrieve 1X9W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1X9W from S2C, [Save to disk]
  • Re-refined 1x9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1X9W 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 1X9W
  • 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 1X9W, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1x9wa1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1x9wa2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1x9wb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1x9w 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: [1x9w_C] [1x9w] [1x9w_D] [1x9w_A] [1x9w_B]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1X9W: [POLAc ] by SMART
  • Other resources with information on 1X9W
  • Community annotation for 1X9W 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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