4O8M Crystal structure of a trap periplasmic solute binding protein actinobacillus succinogenes 130z, target EFI-510004, with bound L-galactonate date 2013-12-28
authors Vetting, M.W., Obaidi, N.F.Al., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Attonito, J.D., Glenn, A.Scott., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Almo, S.C., EFI, Enzyme.Function.Initiative.
compound source
symmetry
R_factor
R_Free 0.2358
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.70
ligand 2Q2, CL, SO4 enzyme
Gene ASUC
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


Primary referenceExperimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes., Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC, Biochemistry. 2015 Jan 27;54(3):909-31. doi: 10.1021/bi501388y. Epub 2015 Jan 16. PMID:25540822
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1226 Kb) [Save to disk]
  • Biological Unit Coordinates (4o8m.pdb1.gz) 159 Kb
  • Biological Unit Coordinates (4o8m.pdb2.gz) 157 Kb
  • Biological Unit Coordinates (4o8m.pdb3.gz) 158 Kb
  • Biological Unit Coordinates (4o8m.pdb4.gz) 156 Kb
  • Biological Unit Coordinates (4o8m.pdb5.gz) 157 Kb
  • Biological Unit Coordinates (4o8m.pdb6.gz) 157 Kb
  • Biological Unit Coordinates (4o8m.pdb7.gz) 158 Kb
  • Biological Unit Coordinates (4o8m.pdb8.gz) 157 Kb
  • LPC: Ligand-Protein Contacts for 4O8M
  • CSU: Contacts of Structural Units for 4O8M
  • Structure Factors (7475 Kb)
  • Retrieve 4O8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4O8M from S2C, [Save to disk]
  • Re-refined 4o8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4O8M 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 4O8M
  • 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 4O8M, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4o8m_C] [4o8m_G] [4o8m] [4o8m_E] [4o8m_F] [4o8m_A] [4o8m_H] [4o8m_D] [4o8m_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4O8M
  • Community annotation for 4O8M at PDBWiki (http://pdbwiki.org)

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