1L5U Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 12 base pairs of duplex DNA following addition of a dTTP, a dATP, and a dCTP residue. date
authors Johnson, S.J., Taylor, J.S., Beese, L.S.
compound source
symmetry
R_factor
R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.95
ligand FRU, GLC, MG, SO4 enzyme
related structures by homologous chain: 1LV5, 3BDP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceProcessive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations., Johnson SJ, Taylor JS, Beese LS, Proc Natl Acad Sci U S A 2003 Apr 1;100(7):3895-900. PMID:12649320
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (1l5u.pdb1.gz) 113 Kb
  • LPC: Ligand-Protein Contacts for 1L5U
  • CSU: Contacts of Structural Units for 1L5U
  • Likely Quarternary Molecular Structure file(s) for 1L5U
  • Structure Factors (672 Kb)
  • Retrieve 1L5U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L5U from S2C, [Save to disk]
  • Re-refined 1l5u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1L5U 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 1L5U
  • 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 1L5U, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l5ua1, region A:297-468 [Jmol] [rasmolscript] [script source]
        - Domain d1l5ua2, region A:469-876 [Jmol] [rasmolscript] [script source]
  • Fold representative 1l5u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1l5u_B] [1l5u_A] [1l5u_C] [1l5u]
  • SWISS-PROT database: [P52026]
  • Domain organization of [DPO1_BACST] by SWISSPFAM
  • Domains found in 1L5U: [35EXOc] [POLAc ] by SMART
  • Other resources with information on 1L5U
  • Community annotation for 1L5U 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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