1P59 Hydrolase Dna date Apr 25, 2003
title Structure Of A Non-Covalent Endonuclease III-Dna Complex
authors J.C.Fromme, G.L.Verdine
compound source
Molecule: 5'-D(Apapgpapcpgp(5iu)Pgpgpapc)-3'
Chain: B
Engineered: Yes
 Synthetic: Yes

Molecule: 5'-D(Tpgp(5iu)Pcpcpap(3dr)Pgp(5iu)Pcpt)
Chain: C
Engineered: Yes
Synthetic: Yes

Molecule: Endonuclease III
Chain: A
Engineered: Yes
Organism_scientific: Geobacillus Stearothermophilus
Organism_taxid: 1422
Gene: Nth
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(C41)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: P 21 21 2
R_factor 0.214 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.321 105.896 41.518 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 3DR, 5IU, NA, SF4 enzyme
related structures by homologous chain: 1ORP
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of a trapped endonuclease III-DNA covalent intermediate., Fromme JC, Verdine GL, EMBO J 2003 Jul 1;22(13):3461-71. PMID:12840008
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (48 Kb) [Save to disk]
  • Biological Unit Coordinates (1p59.pdb1.gz) 43 Kb
  • LPC: Ligand-Protein Contacts for 1P59
  • CSU: Contacts of Structural Units for 1P59
  • Likely Quarternary Molecular Structure file(s) for 1P59
  • Structure Factors (212 Kb)
  • Retrieve 1P59 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1P59 from S2C, [Save to disk]
  • Re-refined 1p59 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1P59 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 1P59
  • 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
  • 3D motif for 1P59, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1p59a_, region A [Jmol] [rasmolscript] [script source]
  • 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: [1p59_A] [1p59_B] [1p59] [1p59_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1P59: [ENDO3c] [FES] [HhH1 ] by SMART
    • Other resources with information on 1P59
  • Community annotation for 1P59 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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