5XD2 Hydrolase date Mar 24, 2017
title Crystal Structure Of Mycobacterium Smegmatis Mutt1 In Comple Ap5a, Atp And Manganese
authors S.M.Arif, U.Varshney, M.Vijayan
compound source
Molecule: Nudix Family Protein
Chain: A
Engineered: Yes
 Organism_scientific: Mycobacterium Smegmatis (Strain Atcc 7 Mc(2)155);
Organism_taxid: 246196
Strain: Atcc 700084 Mc(2)155
Gene: Msmeg_2390
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jw0097
symmetry Space Group: P 1 21 1
R_factor 0.178 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
42.160 83.930 43.640 90.00 93.63 90.00
method X-Ray Diffractionresolution 1.75 Å
ligand 5FA, ATP, GOL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceHydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1., Arif SM, Varshney U, Vijayan M, J Struct Biol. 2017 Jul 10. pii: S1047-8477(17)30122-3. doi:, 10.1016/j.jsb.2017.07.002. PMID:28705712
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (5xd2.pdb1.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 5XD2
  • CSU: Contacts of Structural Units for 5XD2
  • Structure Factors (1432 Kb)
  • Retrieve 5XD2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XD2 from S2C, [Save to disk]
    • View 5XD2 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 5XD2
  • 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
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1t5xd2, region D:122-239 [Jmol] [rasmolscript] [script source]
        - Domain d1g5xd2, region D:254-404 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xd2_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5XD2
  • Community annotation for 5XD2 at PDBWiki (http://pdbwiki.org)

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