4DBX Crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA date 2012-01-16
authors Stogios, P.J., Minasov, G., Tan, K., Nocek, B., Singer, A.U., Evdokimova, E., Egorova, E., Leo, R.Di., Li, H., Shakya, T., Wright, G.D., Savchenko, A., Anderson, W.F., MCSG, Midwest.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.2290
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.00
ligand MSE enzyme
note 4DBX supersedes 3R7Z, 3LZH
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA small molecule discrimination map of the antibiotic resistance kinome., Shakya T, Stogios PJ, Waglechner N, Evdokimova E, Ejim L, Blanchard JE, McArthur AG, Savchenko A, Wright GD, Chem Biol. 2011 Dec 23;18(12):1591-601. PMID:22195561
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (4dbx.pdb1.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 4DBX
  • CSU: Contacts of Structural Units for 4DBX
  • Structure Factors (179 Kb)
  • Retrieve 4DBX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DBX from S2C, [Save to disk]
  • Re-refined 4dbx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DBX 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 4DBX
  • 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 4DBX, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dbx_A] [4dbx]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4DBX
  • Community annotation for 4DBX at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science