3ISB Transferase Dna date Aug 25, 2009
title Binary Complex Of Human Dna Polymerase Beta With A Gapped Dna
authors W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson
compound source
Molecule: Dna Polymerase Beta
Chain: A
Ec:, 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_vector_type: Plasmid
Expression_system_plasmid: Pwl11

Molecule: 5'- D(Cpcpgpapcpgpgpcpgpcpaptpcpapgpc)-3';
Chain: T
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Sytnthesized Oligonucleotide

Molecule: 5'-D(Gpcptpgpaptpgpcpgpc)-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Sytnthesized Oligonucleotide

Molecule: 5'-D(Pgptpcpgpg)-3'
Chain: D
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Sytnthesized Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.211 R_Free 0.271
length a length b length c angle alpha angle beta angle gamma
54.380 79.240 54.880 90.00 105.49 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand NA, SO4 enzyme Transferase E.C. BRENDA

Primary referenceDNA polymerase beta substrate specificity: side chain modulation of the "A-rule"., Beard WA, Shock DD, Batra VK, Pedersen LC, Wilson SH, J Biol Chem. 2009 Nov 13;284(46):31680-9. Epub 2009 Sep 15. PMID:19759017
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3isb.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 3ISB
  • CSU: Contacts of Structural Units for 3ISB
  • Structure Factors (235 Kb)
  • Retrieve 3ISB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ISB from S2C, [Save to disk]
  • Re-refined 3isb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ISB 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 3ISB
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3ISB, from MSDmotif at EBI
  • Fold representative 3isb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3isb] [3isb_P] [3isb_T] [3isb_A] [3isb_D]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 3ISB: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3ISB
  • Community annotation for 3ISB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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