2HR6 Hydrolase date Jul 19, 2006
title Crystal Structure Of Dutpase In Complex With Substrate Analo And Manganese
authors O.Barabas, J.Kovari, R.Tapai, B.G.Vertessy
compound source
Molecule: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase
Chain: A
Synonym: Dutpase, Dutp Pyrophosphatase
Ec: 3.6.1.23
Engineered: 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 0.151 R_Free 0.173
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.049 75.049 99.936 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.84 Å
ligand DUD, EDO, MN enzyme Hydrolase E.C.3.6.1.23 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMethylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site., Kovari J, Barabas O, Varga B, Bekesi A, Tolgyesi F, Fidy J, Nagy J, Vertessy BG, Proteins. 2008 Apr;71(1):308-19. PMID:17932923
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (2hr6.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 2HR6
  • CSU: Contacts of Structural Units for 2HR6
  • Likely Quarternary Molecular Structure file(s) for 2HR6
  • Structure Factors (217 Kb)
  • Retrieve 2HR6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2HR6 from S2C, [Save to disk]
  • Re-refined 2hr6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2HR6 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 2HR6
  • 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 2HR6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2hr6_A] [2hr6]
  • SWISS-PROT database: [P06968]
  • Domain organization of [DUT_ECOLI] by SWISSPFAM
  • Other resources with information on 2HR6
  • Community annotation for 2HR6 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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