3SHD Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1 date
authors Hong, M.K., Kim, J.K., Kang, L.W.
compound source
symmetry
R_factor
R_Free 0.29147
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
ligand MN, SO4 enzyme
Gene APECO1 ; ECOK1
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, K, E, B, H, C, D, I, G, L


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (314 Kb) [Save to disk]
  • Biological Unit Coordinates (3shd.pdb1.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb2.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb3.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb4.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb5.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb6.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb7.gz) 31 Kb
  • Biological Unit Coordinates (3shd.pdb8.gz) 30 Kb
  • Biological Unit Coordinates (3shd.pdb9.gz) 31 Kb
  • LPC: Ligand-Protein Contacts for 3SHD
  • CSU: Contacts of Structural Units for 3SHD
  • Structure Factors (1586 Kb)
  • Retrieve 3SHD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3SHD from S2C, [Save to disk]
  • Re-refined 3shd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3SHD 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 3SHD
  • 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 3SHD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3shd_H] [3shd_A] [3shd_D] [3shd_J] [3shd_G] [3shd_C] [3shd_K] [3shd_L] [3shd_E] [3shd_I] [3shd] [3shd_B] [3shd_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3SHD
  • Community annotation for 3SHD at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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