3UXP Transferase, Lyase Dna date Dec 05, 2011
title Co-Crystal Structure Of Rat Dna Polymerase Beta Mutator I260 Dna-Ddttp
authors C.L.Gridley, J.Jaeger
compound source
Molecule: Dna Polymerase Beta
Chain: A, B
Ec:, 4.2.99.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Polb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna 5'-D(Paptpgptpgpapg)-3'
Chain: P, D
Engineered: Yes
Other_details: Primer Dna Strand

Synthetic: Yes
Other_details: Primer Dna Strand

Molecule: Dna 5'-D(Papcptpcpapcpaptpa)-3'
Chain: T, E
Engineered: Yes
Other_details: Template Dna Strand

Synthetic: Yes
Other_details: Template Dna Strand
symmetry Space Group: P 1 21 1
R_factor 0.218 R_Free 0.292
length a length b length c angle alpha angle beta angle gamma
100.321 56.607 93.144 90.00 102.04 90.00
method X-Ray Diffractionresolution 2.72 Å
ligand D3T, NA enzyme Transferase E.C. BRENDA
A, B

Primary referenceStructural changes in the hydrophobic hinge region adversely affect the activity and fidelity of the I260Q mutator DNA polymerase beta., Gridley CL, Rangarajan S, Firbank S, Dalal S, Sweasy JB, Jaeger J, Biochemistry. 2013 Jun 25;52(25):4422-32. doi: 10.1021/bi301368f. Epub 2013 Jun, 12. PMID:23651085
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (259 Kb) [Save to disk]
  • Biological Unit Coordinates (3uxp.pdb1.gz) 126 Kb
  • Biological Unit Coordinates (3uxp.pdb2.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 3UXP
  • CSU: Contacts of Structural Units for 3UXP
  • Structure Factors (306 Kb)
  • Retrieve 3UXP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UXP from S2C, [Save to disk]
  • Re-refined 3uxp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UXP 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 3UXP
  • 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 3UXP, from MSDmotif at EBI
  • Fold representative 3uxp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3uxp_A] [3uxp_D] [3uxp_P] [3uxp_B] [3uxp_E] [3uxp_T] [3uxp]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3UXP: [HhH1] [POLXc ] by SMART
  • Other resources with information on 3UXP
  • Community annotation for 3UXP at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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