1SMC Hydrolase date Mar 09, 2004
title Mycobacterium Tuberculosis Dutpase Complexed With Dutp In Th Of Metal Ion.
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 0.165 R_Free 0.207
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.595 77.697 94.781 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand DUT, NO3, TRS enzyme Hydrolase E.C.3.6.1.23 BRENDA
related structures by homologous chain: 1MQ7, 1SM8
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 (1smc.pdb1.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 1SMC
  • CSU: Contacts of Structural Units for 1SMC
  • Likely Quarternary Molecular Structure file(s) for 1SMC
  • Structure Factors (171 Kb)
  • Retrieve 1SMC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SMC from S2C, [Save to disk]
  • Re-refined 1smc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SMC 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 1SMC
  • 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 1SMC, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1smca_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1smcb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1smcc_, 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: [1smc_B] [1smc] [1smc_A] [1smc_C]
  • SWISS-PROT database: [P0A552]
  • Domain organization of [DUT_MYCTU] by SWISSPFAM
  • Other resources with information on 1SMC
  • Community annotation for 1SMC 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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