5V1F Transferase Dna, Ligase Dna date Mar 02, 2017
title Dna Polymerase Beta Substrate Complex With 8-Oxog At The Pri Terminus And Incoming Dctp
authors B.D.Freudenthal, M.R.Smith, M.A.Schaich, A.M.Whitaker
compound source
Molecule: Dna (5'-D(Cpcpgpapcpgpcpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgp(8og))-3')
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna Polymerase Beta
Chain: A
Ec: 2.7.7.7,4.2.99.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.226 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.218 79.016 55.626 90.00 107.01 90.00
method X-Ray Diffractionresolution 2.18 Å
ligand 8OG, CA, DCP enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCapturing a mammalian DNA polymerase extending from an oxidized nucleotide., Whitaker AM, Smith MR, Schaich MA, Freudenthal BD, Nucleic Acids Res. 2017 Apr 26. doi: 10.1093/nar/gkx293. PMID:28449123
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (5v1f.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 5V1F
  • CSU: Contacts of Structural Units for 5V1F
  • Structure Factors (265 Kb)
  • Retrieve 5V1F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5V1F from S2C, [Save to disk]
  • Re-refined 5v1f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5V1F 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 5V1F
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5v1f_A] [5v1f_D] [5v1f_P] [5v1f] [5v1f_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5V1F
  • Community annotation for 5V1F at PDBWiki (http://pdbwiki.org)

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