1SKR Transferase Electron Transport Dna date Mar 05, 2004
title T7 Dna Polymerase Complexed To Dna Primertemplate And Ddatp
authors Y.Li, S.Dutta, S.Doublie, H.M.Bdour, J.S.Taylor, T.Ellenberger
compound source
Molecule: 5'-D(Cpgpapapapapcpgpapcgpgpcpcpap Cpcpap(2da))-3';
Chain: P
Engineered: Yes
Other_details: Dna Primer
 Synthetic: Yes

Molecule: 5'-D(Cpcpcptptptpgpgpcpapcptpgpgpc Cpgptptptptpcpg)-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
Synonym: Trx1, Trx
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Trxa, Tsnc, Fipa, B3781, C4701, Z5291, Ecs4714, Stm39 Stmd1.75, Sty3639, T3381, Sf3854, S3905;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 2
R_factor 0.226 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.506 214.020 52.036 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 2DA, DAD, MG enzyme Transferase E.C.2.7.7.7 BRENDA
related structures by homologous chain: 1SL2, 1TKD
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] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (1skr.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 1SKR
  • CSU: Contacts of Structural Units for 1SKR
  • Likely Quarternary Molecular Structure file(s) for 1SKR
  • Structure Factors (442 Kb)
  • Retrieve 1SKR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SKR from S2C, [Save to disk]
  • Re-refined 1skr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1SKR 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 1SKR
  • 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 1SKR, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1skra1, region A:1-210 [Jmol] [rasmolscript] [script source]
        - Domain d1skra2, region A:211-704 [Jmol] [rasmolscript] [script source]
        - Domain d1skrb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1skr 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: [1skr_B] [1skr_T] [1skr_P] [1skr_A] [1skr]
  • SWISS-PROT database: [P00581] [P0AA25]
  • Domain organization of [DPOL_BPT7] [THIO_ECOLI] by SWISSPFAM
  • Domain found in 1SKR: [POLAc ] by SMART
    • Other resources with information on 1SKR
  • Community annotation for 1SKR 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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