4P4P Transferase Dna date Mar 12, 2014
title Crystal Structure Of Leishmania Infantum Polymerase Beta: Ni
authors E.Mejia, M.Burak, A.Alonso, V.Larraga, T.Kunkel, K.Bebenek, M.Garc
compound source
Molecule: Dna Polymerase Beta
Chain: A
Engineered: Yes
Organism_scientific: Leishmania Infantum
Organism_taxid: 5671
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pcpgpgpcpapgptpapcptpg)-3')
Chain: B
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 65 2 2
R_factor 0.191 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.497 106.497 159.609 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • DNA polymerase activity


  • Primary referenceStructures of the Leishmania infantum polymerase beta., Mejia E, Burak M, Alonso A, Larraga V, Kunkel TA, Bebenek K, Garcia-Diaz M, DNA Repair (Amst). 2014 Jun;18:1-9. doi: 10.1016/j.dnarep.2014.03.001. Epub 2014 , Mar 22. PMID:24666693
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (4p4p.pdb1.gz) 106 Kb
  • LPC: Ligand-Protein Contacts for 4P4P
  • CSU: Contacts of Structural Units for 4P4P
  • Structure Factors (343 Kb)
  • Retrieve 4P4P in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P4P from S2C, [Save to disk]
  • Re-refined 4p4p structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P4P 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 4P4P
  • 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 4P4P, from MSDmotif at EBI
  • Fold representative 4p4p from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p4p_B] [4p4p] [4p4p_A] [4p4p_C] [4p4p_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P4P: [HhH1] [POLXc ] by SMART
  • Other resources with information on 4P4P
  • Community annotation for 4P4P at PDBWiki (http://pdbwiki.org)

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