1Q9Y CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA date
authors Freisinger, E., Grollman, A.P., Miller, H., Kisker, C.
compound source
symmetry
R_factor
R_Free 0.27067
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.80
ligand 8OG, CA, DCP, DOC enzyme
related structures by homologous chain: 1CLQ, 1WAJ
Gene
Ontology
ChainFunctionProcessComponent
A
  • DNA-directed DNA polymerase ...
  • nuclease activity
  • exonuclease activity
  • 3'-5' exonuclease activity


  • Primary referenceLesion (in)tolerance reveals insights into DNA replication fidelity., Freisinger E, Grollman AP, Miller H, Kisker C, EMBO J 2004 Apr 7;23(7):1494-505. Epub 2004 Apr 1. PMID:15057282
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (344 Kb) [Save to disk]
  • Biological Unit Coordinates (1q9y.pdb1.gz) 328 Kb
  • LPC: Ligand-Protein Contacts for 1Q9Y
  • CSU: Contacts of Structural Units for 1Q9Y
  • Likely Quarternary Molecular Structure file(s) for 1Q9Y
  • Structure Factors (255 Kb)
  • Retrieve 1Q9Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Q9Y from S2C, [Save to disk]
  • Re-refined 1q9y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Q9Y 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 1Q9Y
  • 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 1Q9Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1q9ya1, region A:1-375 [Jmol] [rasmolscript] [script source]
        - Domain d1q9ya2, region A:376-902 [Jmol] [rasmolscript] [script source]
  • Fold representative 1q9y 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: [1q9y_A] [1q9y] [1q9y_P] [1q9y_T]
  • SWISS-PROT database: [Q38087]
  • Domain organization of [DPOL_BPR69] by SWISSPFAM
  • Domain found in 1Q9Y: [POLBc ] by SMART
  • Other resources with information on 1Q9Y
  • Community annotation for 1Q9Y 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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