5UGO Transferase Dna date Jan 09, 2017
title Dna Polymerase Beta Nick Complex With Imidodiphosphate
authors B.D.Freudenthal, S.H.Wilson, W.A.Beard
compound source
Molecule: Dna (5'-D(Cpcpgpapcpgpgpcpgpcpaptpcp 3');
Chain: T
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpcpc)-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 K-12
Expression_system_taxid: 83333
symmetry Space Group: P 1 21 1
R_factor 0.179 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.596 79.312 55.194 90.00 107.55 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 2PN, CA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceModulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction., Shock DD, Freudenthal BD, Beard WA, Wilson SH, Nat Chem Biol. 2017 Jul 31. doi: 10.1038/nchembio.2450. PMID:28759020
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (79 Kb) [Save to disk]
  • Biological Unit Coordinates (5ugo.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 5UGO
  • CSU: Contacts of Structural Units for 5UGO
  • Structure Factors (291 Kb)
  • Retrieve 5UGO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UGO from S2C, [Save to disk]
  • Re-refined 5ugo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5UGO 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 5UGO
  • 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: [5ugo_A] [5ugo_D] [5ugo_P] [5ugo_T]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5UGO
  • Community annotation for 5UGO at PDBWiki (http://pdbwiki.org)

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