1SNF Hydrolase date Mar 10, 2004
title Mycobacterium Tuberculosis Dutpase Complexed With Magnesium Deoxyuridine 5'-Monophosphate
authors M.R.Sawaya, S.Chan, B.Segelke, T.Lekin, H.Krupka, U.S.Cho, M.Y.Ki C.Y.Kim, C.M.Naranjo, Y.C.Rogers, M.S.Park, G.S.Waldo, I.Pashko D.Cascio, T.O.Yeates, J.L.Perry, T.C.Terwilliger, D.Eisenberg, T Structural Genomics Consortium (Tbsgc)
compound source
Molecule: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase
Chain: A, B, C
Synonym: Dutpase, Dutp Pyrophosphatase
Ec: 3.6.1.23
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis
Organism_taxid: 1773
Gene: Dut, Rv2697c, Mt2771, Mtcy05a6.18c, Mb2716c
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21pro
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet28b
symmetry Space Group: P 21 21 21
R_factor 0.169 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.228 77.496 93.949 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand MG, NO3, TRS, UMP enzyme Hydrolase E.C.3.6.1.23 BRENDA
related structures by homologous chain: 1MQ7, 1SJN
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism., Chan S, Segelke B, Lekin T, Krupka H, Cho US, Kim MY, So M, Kim CY, Naranjo CM, Rogers YC, Park MS, Waldo GS, Pashkov I, Cascio D, Perry JL, Sawaya MR, J Mol Biol 2004 Aug 6;341(2):503-17. PMID:15276840
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (1snf.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 1SNF
  • CSU: Contacts of Structural Units for 1SNF
  • Likely Quarternary Molecular Structure file(s) for 1SNF
  • Structure Factors (234 Kb)
  • Retrieve 1SNF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SNF from S2C, [Save to disk]
  • Re-refined 1snf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SNF 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 1SNF
  • 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 1SNF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1snfa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1snfb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1snfc_, region C [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: [1snf_A] [1snf] [1snf_C] [1snf_B]
  • SWISS-PROT database: [P0A552]
  • Domain organization of [DUT_MYCTU] by SWISSPFAM
  • Other resources with information on 1SNF
  • Community annotation for 1SNF 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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