5VS4 Transferase, Lyase Dna date May 11, 2017
title Human Dna Polymerase Beta 8-Oxog:Da Extension With Dttp Afte
authors A.J.Reed, Z.Suo
compound source
Molecule: Dna (5'-D(Cpcpgpapcpap(8og) Pgpcpgpcpaptpcpapg)-3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cptpgpaptpgpcpgpcpapt)-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 0.199 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.800 79.700 55.300 90.00 107.10 90.00
method X-Ray Diffractionresolution 1.87 Å
ligand 8OG, ACT, MG, PPV enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceTime-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta., Reed AJ, Suo Z, J Am Chem Soc. 2017 Jul 19;139(28):9684-9690. doi: 10.1021/jacs.7b05048. Epub, 2017 Jul 6. PMID:28682600
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (5vs4.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 5VS4
  • CSU: Contacts of Structural Units for 5VS4
  • Structure Factors (268 Kb)
  • Retrieve 5VS4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VS4 from S2C, [Save to disk]
  • Re-refined 5vs4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VS4 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 5VS4
  • 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
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vs4_A] [5vs4_D] [5vs4_T] [5vs4_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VS4
  • Community annotation for 5VS4 at PDBWiki (http://pdbwiki.org)

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science