5CMS Structural Insights into the Mechanism of Escherichia coli Ymdb date
authors Zhang, W., Wang, C., Song, Y., Shao, C., Zhang, X., Zang, J.
compound source
symmetry
R_factor
R_Free 0.24970
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.98
ligand APR, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, Q, M, C, L, A, J, O, P, B, H, D, R, I, G


Primary referenceStructural insights into the mechanism of Escherichia coli YmdB: A 2'-O-acetyl-ADP-ribose deacetylase., Zhang W, Wang C, Song Y, Shao C, Zhang X, Zang J, J Struct Biol. 2015 Dec;192(3):478-86. doi: 10.1016/j.jsb.2015.10.010. Epub 2015 , Oct 19. PMID:26481419
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (490 Kb) [Save to disk]
  • Biological Unit Coordinates (5cms.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (5cms.pdb2.gz) 33 Kb
  • Biological Unit Coordinates (5cms.pdb3.gz) 34 Kb
  • Biological Unit Coordinates (5cms.pdb4.gz) 33 Kb
  • Biological Unit Coordinates (5cms.pdb5.gz) 33 Kb
  • Biological Unit Coordinates (5cms.pdb6.gz) 33 Kb
  • Biological Unit Coordinates (5cms.pdb7.gz) 33 Kb
  • Biological Unit Coordinates (5cms.pdb8.gz) 32 Kb
  • Biological Unit Coordinates (5cms.pdb9.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 5CMS
  • CSU: Contacts of Structural Units for 5CMS
  • Structure Factors (2094 Kb)
  • Retrieve 5CMS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CMS from S2C, [Save to disk]
  • Re-refined 5cms structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5CMS 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 5CMS
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cms_O] [5cms_A] [5cms_B] [5cms_F] [5cms_K] [5cms_P] [5cms_N] [5cms] [5cms_J] [5cms_E] [5cms_R] [5cms_Q] [5cms_M] [5cms_H] [5cms_C] [5cms_G] [5cms_L] [5cms_I] [5cms_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5CMS: [A1pp ] by SMART
    • Other resources with information on 5CMS
  • Community annotation for 5CMS at PDBWiki (http://pdbwiki.org)

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