4KHY Transferase Dna date May 01, 2013
title Ternary Complex Of Rb69 Mutant L415f With Ribonucleotide At Position
authors A.R.Clausen, L.C.Pedersen
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: Dnarna (5'-D(Apcpapgpg)-R(Pu)- D(Papapgpcpapgptpcpcpgpcpg)-3');
Chain: T
Engineered: Yes
Other_details: Template Strand

Synthetic: Yes

Molecule: Dna (5'-D(Gpcpgpgpapcptpgpcptptpapcp
Chain: P
Engineered: Yes
Other_details: Primer Strand

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.198 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.795 118.240 127.610 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.25 Å
ligand CA, NA, TTP 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-function analysis of ribonucleotide bypass by B family DNA replicases., Clausen AR, Murray MS, Passer AR, Pedersen LC, Kunkel TA, Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16802-7. doi:, 10.1073/pnas.1309119110. Epub 2013 Sep 30. PMID:24082122
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (349 Kb) [Save to disk]
  • Biological Unit Coordinates (4khy.pdb1.gz) 340 Kb
  • LPC: Ligand-Protein Contacts for 4KHY
  • CSU: Contacts of Structural Units for 4KHY
  • Structure Factors (527 Kb)
  • Retrieve 4KHY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KHY from S2C, [Save to disk]
  • Re-refined 4khy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KHY 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 4KHY
  • 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 4KHY, from MSDmotif at EBI
  • Fold representative 4khy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4khy] [4khy_P] [4khy_A] [4khy_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4KHY: [POLBc ] by SMART
  • Other resources with information on 4KHY
  • Community annotation for 4KHY at PDBWiki (http://pdbwiki.org)

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