5BOM Transferase, Lyase Dna date May 27, 2015
title Dna Polymerase Beta Binary Complex With A Templating 5clc
authors B.D.Freudenthal, S.H.Wilson
compound source
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_plasmid: Pwl11

Molecule: Dna (5'-D(Pgptpcpgpg)-3')
Chain: D
Engineered: Yes
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(Cpcpgpapcp(4u3) Pgpcpgpcpaptpcpapgpc)-3');
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.190 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.944 79.547 55.133 90.00 109.23 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand 4U3, 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] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (5bom.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 5BOM
  • CSU: Contacts of Structural Units for 5BOM
  • Structure Factors (464 Kb)
  • Retrieve 5BOM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5BOM from S2C, [Save to disk]
  • Re-refined 5bom structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5BOM 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 5BOM
  • 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: [5bom_T] [5bom_D] [5bom] [5bom_P] [5bom_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5BOM: [HhH1] [POLXc ] by SMART
    • Other resources with information on 5BOM
  • Community annotation for 5BOM at PDBWiki (http://pdbwiki.org)

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