4GKI Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor 1-NM-PP1 date 2012-08-11
authors Stogios, P.J., Evdokimova, E., Wawrzak, Z., Minasov, G., Egorova, O., Leo, R.Di., Shakya, T., Spanogiannopoulos, P., Todorovic, N., Capretta, A., Wright, G.D., Savchenko, A., Anderson, W.F., CSGID, Center.for.Structural.Genomics.of.Infectious.Diseases.
compound source
R_Free 0.2158
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.88
ligand 0JN, ACT, CL, KAN, MSE, NA, PEG enzyme
F, A, J, K, E, B, H, C, D, I, G, L

Primary referenceStructure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance., Stogios PJ, Spanogiannopoulos P, Evdokimova E, Egorova O, Shakya T, Todorovic N, Capretta A, Wright GD, Savchenko A, Biochem J. 2013 Jun 12. PMID:23758273
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1204 Kb) [Save to disk]
  • Biological Unit Coordinates (4gki.pdb1.gz) 112 Kb
  • Biological Unit Coordinates (4gki.pdb2.gz) 108 Kb
  • Biological Unit Coordinates (4gki.pdb3.gz) 113 Kb
  • Biological Unit Coordinates (4gki.pdb4.gz) 106 Kb
  • Biological Unit Coordinates (4gki.pdb5.gz) 111 Kb
  • Biological Unit Coordinates (4gki.pdb6.gz) 108 Kb
  • Biological Unit Coordinates (4gki.pdb7.gz) 113 Kb
  • Biological Unit Coordinates (4gki.pdb8.gz) 107 Kb
  • Biological Unit Coordinates (4gki.pdb9.gz) 105 Kb
  • LPC: Ligand-Protein Contacts for 4GKI
  • CSU: Contacts of Structural Units for 4GKI
  • Structure Factors (4454 Kb)
  • Retrieve 4GKI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GKI from S2C, [Save to disk]
  • Re-refined 4gki structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4GKI 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 4GKI
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4GKI, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gki_E] [4gki_F] [4gki_K] [4gki_H] [4gki] [4gki_L] [4gki_J] [4gki_G] [4gki_I] [4gki_D] [4gki_B] [4gki_C] [4gki_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4GKI
  • Community annotation for 4GKI at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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