2P66 Transferase, Lyase Dna date Mar 16, 2007
title Human Dna Polymerase Beta Complexed With Tetrahydrofuran (Abasic Site) Containing Dna
authors R.Prasad, V.K.Batra, X.P.Yang, J.M.Krahn, L.C.Pedersen, W.A.Beard, S.H.Wilson
compound source
Molecule: Dna (5'- D(Cpcpgpapcpapgpcpgpcpaptpcpapgpc)-3');
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Gpcptpgpaptpgpcpgpcpc)-3')
Chain: C
Engineered: Yes

Synthetic: Yes

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

Synthetic: Yes

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
symmetry Space Group: P 1 21 1
R_factor 0.217 R_Free 0.280
length a length b length c angle alpha angle beta angle gamma
55.700 81.100 54.900 90.00 108.60 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 3DR, NA, PO4 enzyme Transferase E.C. BRENDA

Primary referenceStructural insight into the DNA polymerase beta deoxyribose phosphate lyase mechanism., Prasad R, Batra VK, Yang XP, Krahn JM, Pedersen LC, Beard WA, Wilson SH, DNA Repair (Amst). 2005 Dec 8;4(12):1347-57. Epub 2005 Sep 19. PMID:16172026
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (74 Kb) [Save to disk]
  • Biological Unit Coordinates (2p66.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 2P66
  • CSU: Contacts of Structural Units for 2P66
  • Likely Quarternary Molecular Structure file(s) for 2P66
  • Structure Factors (232 Kb)
  • Retrieve 2P66 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2P66 from S2C, [Save to disk]
  • Re-refined 2p66 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2P66 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 2P66
  • 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 2P66, from MSDmotif at EBI
  • Fold representative 2p66 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2p66] [2p66_A] [2p66_B] [2p66_D] [2p66_C]
  • SWISS-PROT database: [P06746]
  • Domain organization of [DPOLB_HUMAN] by SWISSPFAM
  • Domains found in 2P66: [HhH1] [POLXc ] by SMART
  • Other resources with information on 2P66
  • Community annotation for 2P66 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science