5C4L

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

• PDB DOI: https://doi.org/10.2210/pdb5C4L/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus casseliflavus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-06-18 Released: 2016-02-03 
• Deposition Author(s): Kaplan, E., Guichou, J.F., Berrou, K., Chaloin, L., Leban, N., Lallemand, P., Barman, T., Serpersu, E.H., Lionne, C.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 

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

• PubMed: 26802312 
• DOI: https://doi.org/10.1016/j.bbagen.2016.01.016
• Primary Citation of Related Structures:  
  5C4K, 5C4L


• 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, 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 75.78 kDa 
• Atom Count: 4,989 
• Modelled Residue Count: 594 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APH(2'')-Id	A, B	321	Enterococcus casseliflavus	Mutation(s): 2  Gene Names: aph(2'')-Id
UniProt
Find proteins for O68183 (Enterococcus casseliflavus) Explore O68183  Go to UniProtKB:  O68183

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIS	D [auth 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 C19 H37 N5 O7 URWAJWIAIPFPJE-YFMIWBNJSA-N
4XR	C [auth A]	(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-ol C6 H12 N2 O2 GBOGEEQLPKNDRP-RITPCOANSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SIS	Binding MOAD:  5C4L	Kd: 2300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.278 
• R-Value Work: 0.227 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.22	α = 90
b = 65.04	β = 91.18
c = 78.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
Coot	model building
DNA	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Kaplan, E., Guichou, J.F., Berrou, K., Chaloin, L., Leban, N., Lallemand, P., Barman, T., Serpersu, E.H., Lionne, C.

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Funding Organization	Location	Grant Number
French National Research Agency	France	FDT20140931113

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Refinement description