6CTZ

Structure of the GDP and kanamycin complex of APH(2")-IIia

• PDB DOI: https://doi.org/10.2210/pdb6CTZ/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Enterococcus gallinarum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-03-23 Released: 2019-03-27 
• Deposition Author(s): Smith, C.A., Vakulenko, S.B.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.171 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 

Literature

Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2''-phosphotransferases

Smith, C.A., Toth, M., Stewart, N.K., Maltz, L., Vakulenko, S.B.

(2019) Acta Crystallogr D Biol Crystallogr 75: 1129-1137

• DOI: https://doi.org/10.1107/S2059798319015079

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.81 kDa 
• Atom Count: 2,914 
• Modelled Residue Count: 297 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gentamicin resistance protein	A	297	Enterococcus gallinarum	Mutation(s): 2
UniProt
Find proteins for P96762 (Enterococcus gallinarum) Explore P96762  Go to UniProtKB:  P96762

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KAN	E [auth A]	KANAMYCIN A C18 H36 N4 O11 SBUJHOSQTJFQJX-NOAMYHISSA-N
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 0.171 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.169	α = 90
b = 58.982	β = 90
c = 70.853	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Smith, C.A., Vakulenko, S.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI057393

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description