4DIE Crystal structure of a cytidylate kinase CmK from Mycobacterium abscessus bound to cytidine-5'-monophosphate date 2012-01-30
authors SSGCID, Seattle.Structural.Genomics.Center.for.Infectious.Disease.
compound source
symmetry
R_factor
R_Free 0.2700
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.65
ligand C5P, PO4 enzyme
note 4DIE is a representative structure
Gene MAB
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • cytidylate kinase activity


  • Primary referenceIncreasing the structural coverage of tuberculosis drug targets., Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ, Tuberculosis (Edinb). 2014 Dec 19. pii: S1472-9792(14)20565-8. doi:, 10.1016/j.tube.2014.12.003. PMID:25613812
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (246 Kb) [Save to disk]
  • Biological Unit Coordinates (4die.pdb1.gz) 119 Kb
  • Biological Unit Coordinates (4die.pdb2.gz) 121 Kb
  • Biological Unit Coordinates (4die.pdb3.gz) 61 Kb
  • Biological Unit Coordinates (4die.pdb4.gz) 61 Kb
  • Biological Unit Coordinates (4die.pdb5.gz) 64 Kb
  • Biological Unit Coordinates (4die.pdb6.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 4DIE
  • CSU: Contacts of Structural Units for 4DIE
  • Structure Factors (462 Kb)
  • Retrieve 4DIE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DIE from S2C, [Save to disk]
  • Re-refined 4die structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DIE 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 4DIE
  • 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 4DIE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4die_D] [4die] [4die_A] [4die_C] [4die_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4DIE
  • Community annotation for 4DIE at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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