4DFU Inhibition of an antibiotic resistance enzyme: crystal structure of aminoglycoside phosphotransferase APH(2")-ID/APH(2")-IVA in complex with kanamycin inhibited with quercetin date 2012-01-24
authors Stogios, P.J., Minasov, G., Dong, A., Evdokimova, E., Egorova, E., Leo, R.Di., Li, H., Shakya, T., Wright, G.D., Savchenko, A., Anderson, W.F., CSGID, Center.for.Structural.Genomics.of.Infectious.Diseases.
compound source
symmetry
R_factor
R_Free 0.2697
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.98
ligand CL, KAN, MSE, QUE enzyme
note 4DFU supersedes 3VCQ, 3R82
Gene
Ontology
ChainFunctionProcessComponent
A, B


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] (215 Kb) [Save to disk]
  • Biological Unit Coordinates (4dfu.pdb1.gz) 106 Kb
  • Biological Unit Coordinates (4dfu.pdb2.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 4DFU
  • CSU: Contacts of Structural Units for 4DFU
  • Structure Factors (528 Kb)
  • Retrieve 4DFU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DFU from S2C, [Save to disk]
  • Re-refined 4dfu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DFU 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 4DFU
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4DFU, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dfu] [4dfu_A] [4dfu_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4DFU
  • Community annotation for 4DFU at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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