1UT8 Hydrolase date Dec 04, 2003
title Divalent Metal Ions (Zinc) Bound To T5 5'-Exonuclease
authors T.A.Ceska, J.R.Sayers, D.Suck
compound source
Molecule: Exodeoxyribonuclease
Chain: A, B
Synonym: 5'-Exonuclease
Ec: 3.1.11.3
Engineered: Yes
Organism_scientific: Bacteriophage T5
Organism_taxid: 10726
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43
R_factor 0.235 R_Free 0.313
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.940 77.940 134.690 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand ZN enzyme Hydrolase E.C.3.1.11.3 BRENDA
related structures by homologous chain: 1EXN, 1UT5
Gene
Ontology
ChainFunctionProcessComponent
A, B
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • 5'-3' exonuclease activity
  • 5'-3' exodeoxyribonuclease a...


  • Primary referenceRoles of divalent metal ions in flap endonuclease-substrate interactions., Feng M, Patel D, Dervan JJ, Ceska T, Suck D, Haq I, Sayers JR, Nat Struct Mol Biol 2004 May;11(5):450-6. Epub 2004 Apr 11. PMID:15077103
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (96 Kb) [Save to disk]
  • Biological Unit Coordinates (1ut8.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (1ut8.pdb2.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 1UT8
  • CSU: Contacts of Structural Units for 1UT8
  • Likely Quarternary Molecular Structure file(s) for 1UT8
  • Structure Factors (144 Kb)
  • Retrieve 1UT8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UT8 from S2C, [Save to disk]
  • Re-refined 1ut8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1UT8 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 1UT8
  • 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 1UT8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ut8a1, region A:186-291 [Jmol] [rasmolscript] [script source]
        - Domain d1ut8a2, region A:20-185 [Jmol] [rasmolscript] [script source]
        - Domain d1ut8b1, region B:186-291 [Jmol] [rasmolscript] [script source]
        - Domain d1ut8b2, region B:20-185 [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: [1ut8_A] [1ut8] [1ut8_B]
  • SWISS-PROT database: [P06229]
  • Domain organization of [EXO5_BPT5] by SWISSPFAM
  • Domains found in 1UT8: [53EXOc] [HhH2 ] by SMART
  • Other resources with information on 1UT8
  • Community annotation for 1UT8 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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