1RN8 Hydrolase date Dec 01, 2003
title Crystal Structure Of Dutpase Complexed With Substrate Analogue Imido-Dutp
authors O.Barabas, V.Pongracz, J.Kovari, M.Wilmanns, B.G.Vertessy
compound source
Molecule: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase
Chain: A
Synonym: Dutpase, Dutp Pyrophosphatase
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Dut, Dnas, Sof, B3640
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 0.137 R_Free 0.180
length a length b length c angle alpha angle beta angle gamma
74.618 74.618 99.580 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.93 Å
ligand ACT, DUP, MG, TRS enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1DUP, 1SYL

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] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (1rn8.pdb1.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 1RN8
  • CSU: Contacts of Structural Units for 1RN8
  • Likely Quarternary Molecular Structure file(s) for 1RN8
  • Structure Factors (168 Kb)
  • Retrieve 1RN8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RN8 from S2C, [Save to disk]
  • Re-refined 1rn8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RN8 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 1RN8
  • 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 1RN8, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rn8a_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1rn8 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: [1rn8] [1rn8_A]
  • SWISS-PROT database: [P06968]
  • Domain organization of [DUT_ECOLI] by SWISSPFAM
  • Other resources with information on 1RN8
  • Community annotation for 1RN8 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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