5C4K

APH(2")-IVa in complex with GET (G418) at room temperature

PDB DOI: https://doi.org/10.2210/pdb5C4K/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus casseliflavus
Expression System: Escherichia coli BL21
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.199
R-Value Work: 0.159
R-Value Observed: 0.161

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 26802312 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 75.69 kDa
Atom Count: 4,964
Modelled Residue Count: 593
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O68183
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GET Query on GET Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GENETICIN C₂₀ H₄₀ N₄ O₁₀ BRZYSWJRSDMWLG-DJWUNRQOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.199
R-Value Work: 0.159
R-Value Observed: 0.161
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.703	α = 90
b = 64.941	β = 90.73
c = 78.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

Funding Organization	Location	Grant Number
French National Research Agency	France	FDT20140931113

Revision History (Full details and data files)

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