1SYL Hydrolase date Apr 01, 2004
title Crystal Structure Of Inactive Mutant Dutpase Complexed With Dutp
authors O.Barabas, J.Kovari, V.Pongracz, M.Wilmanns, B.G.Vertessy
compound source
Molecule: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase
Chain: A
Synonym: Dutpase, Dutp Pyrophosphatase
Ec: 3.6.1.23
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Dut
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 63 2 2
R_factor 0.158 R_Free 0.189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.421 76.421 100.259 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.95 Å
ligand DUT, MG, TRS enzyme Hydrolase E.C.3.6.1.23 BRENDA
related structures by homologous chain: 1DUD, 1RN8
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase., Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG, J Biol Chem 2004 Jun 17;. PMID:15208312
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (1syl.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 1SYL
  • CSU: Contacts of Structural Units for 1SYL
  • Likely Quarternary Molecular Structure file(s) for 1SYL
  • Structure Factors (95 Kb)
  • Retrieve 1SYL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SYL from S2C, [Save to disk]
  • Re-refined 1syl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SYL 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 1SYL
  • 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 1SYL, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1syla_, 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: [1syl] [1syl_A]
  • SWISS-PROT database: [P06968]
  • Domain organization of [DUT_ECOLI] by SWISSPFAM
  • Other resources with information on 1SYL
  • Community annotation for 1SYL 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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