5C4L

Conformational alternate of sisomicin in complex with APH(2")-IVa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Aminoglycoside binding and catalysis specificity of aminoglycoside 2-phosphotransferase IVa: A thermodynamic, structural and kinetic study.

Kaplan, E.Guichou, J.F.Chaloin, L.Kunzelmann, S.Leban, N.Serpersu, E.H.Lionne, C.

(2016) Biochim.Biophys.Acta 1860: 802-813

  • DOI: 10.1016/j.bbagen.2016.01.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminoglycoside O-phosphotransferases make up a large class of bacterial enzymes that is widely distributed among pathogens and confer a high resistance to several clinically used aminoglycoside antibiotics. Aminoglycoside 2″-phosphotransferase IVa, A ...

    Aminoglycoside O-phosphotransferases make up a large class of bacterial enzymes that is widely distributed among pathogens and confer a high resistance to several clinically used aminoglycoside antibiotics. Aminoglycoside 2″-phosphotransferase IVa, APH(2″)-IVa, is an important member of this class, but there is little information on the thermodynamics of aminoglycoside binding and on the nature of its rate-limiting step.


    Organizational Affiliation

    CNRS, FRE3689 - Université de Montpellier, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, F-34293 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APH(2'')-Id
A, B
321Enterococcus casseliflavusMutation(s): 2 
Gene Names: aph(2'')-Id
Find proteins for O68183 (Enterococcus casseliflavus)
Go to UniProtKB:  O68183
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4XR
Query on 4XR

Download SDF File 
Download CCD File 
A
(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-ol
C6 H12 N2 O2
GBOGEEQLPKNDRP-RITPCOANSA-N
 Ligand Interaction
SIS
Query on SIS

Download SDF File 
Download CCD File 
B
(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
Sisomicin
C19 H37 N5 O7
URWAJWIAIPFPJE-YFMIWBNJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SISKd: 2300 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.220α = 90.00
b = 65.040β = 91.18
c = 78.780γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
SCALAdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondation pour la Recherche MedicaleFranceFDT20140931113

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references