1SKW Transferase Electron Transport Dna date Mar 05, 2004
title Binary 3' Complex Of T7 Dna Polymerase With A Dna Primertemplate Containing A Disordered Cis-Syn Thymine Dimer On The Template
authors Y.Li, S.Dutta, S.Doublie, H.M.Bdour, J.S.Taylor, T.Ellenberger
compound source
Molecule: 5'- D(Cpgpapapapapcpgpapcgpgpcpcpapgptpgpcp Cp(2dt))-3';
Chain: P
Engineered: Yes
Other_details: Dna Primer
Synthetic: Yes

Molecule: 5'-D(Cpcpcp(Ttd) Papgpgpcpapcptpgpgpcpcpgptpcpgptptptptp Cpg)-3';
Chain: T
Engineered: Yes
Other_details: Dna Template

Synthetic: Yes

Molecule: Dna Polymerase
Chain: A
Synonym: T7 Dna Polymerase
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes

Organism_scientific: Enterobacteria Phage T7
Organism_taxid: 10760
Gene: 5
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Thioredoxin 1
Chain: B
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.239 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.718 211.493 52.187 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand 2DT, MG enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1SKS, 1SL2
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • B


    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] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (1skw.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 1SKW
  • CSU: Contacts of Structural Units for 1SKW
  • Likely Quarternary Molecular Structure file(s) for 1SKW
  • Structure Factors (432 Kb)
  • Retrieve 1SKW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SKW from S2C, [Save to disk]
  • Re-refined 1skw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SKW 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 1SKW
  • 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 1SKW, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1skwa1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1skwa2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1skwb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1skw 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: [1skw_P] [1skw_B] [1skw] [1skw_A] [1skw_T]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1SKW: [POLAc ] by SMART
  • Other resources with information on 1SKW
  • Community annotation for 1SKW at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science