5BOL Transferase Dna date May 27, 2015
title Dna Polymerase Beta Ternary Complex With A Templating 5clc A Incoming Dgtp Analog
authors B.D.Freudenthal, S.H.Wilson
compound source
Molecule: Dna (5'-D(Cpcpgpapcp(Cdo) Pgpcpgpcpaptpcpapgpc)-3');
Chain: T
Engineered: Yes
Other_details: Cdo Corresponds To 5-Chlorocytosine Deoxynuc
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpc)-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
Expression_system_strain: Tap56
Expression_system_plasmid: Pwl11
symmetry Space Group: P 1 21 1
R_factor 0.190 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.640 79.114 55.702 90.00 107.65 90.00
method X-Ray Diffractionresolution 1.98 Å
ligand 1GC, 4U3, MG, NA enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceIntrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer., Fedeles BI, Freudenthal BD, Yau E, Singh V, Chang SC, Li D, Delaney JC, Wilson SH, Essigmann JM, Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4571-80. doi:, 10.1073/pnas.1507709112. Epub 2015 Aug 4. PMID:26243878
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (5bol.pdb1.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 5BOL
  • CSU: Contacts of Structural Units for 5BOL
  • Structure Factors (473 Kb)
  • Retrieve 5BOL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BOL from S2C, [Save to disk]
  • Re-refined 5bol structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5BOL 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 5BOL
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5bol from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5bol_D] [5bol] [5bol_A] [5bol_T] [5bol_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5BOL: [HhH1] [POLXc ] by SMART
  • Other resources with information on 5BOL
  • Community annotation for 5BOL at PDBWiki (http://pdbwiki.org)

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