4DTP Transferase Dna date Feb 21, 2012
title Rb69 Dna Polymerase Ternary Complex With Dgtp Opposite An Ab And Ddadt As The Penultimate Base-Pair
authors S.Xia, J.Wang, W.H.Konigsberg
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna Template
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Dna Primer
Chain: P
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.519 118.344 130.730 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand 3DR, CA, DGT enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • Primary referenceContribution of Partial Charge Interactions and Base-Stacking to the Efficiency of Primer-Extension at and beyond Abasic Sites in DNA., Xia S, Vashishtha AK, Bulkley D, Eom SH, Wang J, Konigsberg WH, Biochemistry. 2012 May 25. PMID:22630605
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (346 Kb) [Save to disk]
  • Biological Unit Coordinates (4dtp.pdb1.gz) 339 Kb
  • LPC: Ligand-Protein Contacts for 4DTP
  • CSU: Contacts of Structural Units for 4DTP
  • Structure Factors (1104 Kb)
  • Retrieve 4DTP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DTP from S2C, [Save to disk]
  • Re-refined 4dtp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DTP 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 4DTP
  • 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 4DTP, from MSDmotif at EBI
  • Fold representative 4dtp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dtp_A] [4dtp_P] [4dtp] [4dtp_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DTP: [POLBc ] by SMART
  • Other resources with information on 4DTP
  • Community annotation for 4DTP at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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