3ISD Transferase Dna date Aug 25, 2009
title Ternary Complex Of Human Dna Polymerase Beta With An Abasic (Thf): Dapcpp Mismatch
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: 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_vector_type: Plasmid
Expression_system_plasmid: Pwl11

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Sytnthesized Oligonucleotide

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Sytnthesized Oligonucleotide

Molecule: 5'-D(Cpcpgpapcp(3dr)Pgpcpgpcpaptpcp 3';
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemically Sytnthesized Oligonucleotide
symmetry Space Group: P 1 21 1
R_factor 0.195 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
54.700 77.640 55.220 90.00 113.67 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand 3DR, EDO, F2A, MN, NA BindingDB enzyme Transferase E.C.2.7.7.7 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


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] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3isd.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 3ISD
  • CSU: Contacts of Structural Units for 3ISD
  • Structure Factors (176 Kb)
  • Retrieve 3ISD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ISD from S2C, [Save to disk]
  • Re-refined 3isd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ISD 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 3ISD
  • 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
  • 3D motif for 3ISD, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3isd_A] [3isd_T] [3isd_P] [3isd_D] [3isd]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 3ISD: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3ISD
  • Community annotation for 3ISD 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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