3SUP Transferase Dna date Jul 11, 2011
title Rb69 Dna Polymerase (Y567a) Ternary Complex With Dctp Opposi Rich Sequence)
authors S.Xia, W.H.Konigsberg, J.Wang
compound source
Molecule: Dna Polymerase
Chain: A
Synonym: Gp43
Ec: 2.7.7.7
Engineered: Yes
Mutation: Yes
Organism_scientific: Enterobacteria Phage Rb69
Organism_taxid: 12353
Gene: 43
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 5'-D(Pcp(2pr)Ptpcpgpcpcpgpcpcpgpcpgp 3';
Chain: T
Engineered: Yes
Other_details: Template

Synthetic: Yes

Molecule: 5'-D(Cpgpcpgpcpgpgpcpgpgpcpgp(2da))-
Chain: P
Engineered: Yes
Other_details: Primer

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.200 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.756 120.357 130.823 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.32 Å
ligand 2DA, 2PR, CA, DCP 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 referenceStructure of the 2-Aminopurine-Cytosine Base Pair Formed in the Polymerase Active Site of the RB69 Y567A-DNA Polymerase., Reha-Krantz LJ, Hariharan C, Subuddhi U, Xia S, Zhao C, Beckman J, Christian T, Konigsberg W, Biochemistry. 2011 Nov 22;50(46):10136-49. Epub 2011 Oct 28. PMID:22023103
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (339 Kb) [Save to disk]
  • Biological Unit Coordinates (3sup.pdb1.gz) 332 Kb
  • LPC: Ligand-Protein Contacts for 3SUP
  • CSU: Contacts of Structural Units for 3SUP
  • Structure Factors (554 Kb)
  • Retrieve 3SUP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SUP from S2C, [Save to disk]
  • Re-refined 3sup structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3SUP 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 3SUP
  • 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 3SUP, from MSDmotif at EBI
  • Fold representative 3sup from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3sup_T] [3sup_P] [3sup] [3sup_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3SUP: [POLBc ] by SMART
  • Other resources with information on 3SUP
  • Community annotation for 3SUP at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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