6CTZ | pdb_00006ctz

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.171 (Depositor), 0.171 (DCC)
R-Value Work:
0.146 (Depositor), 0.147 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P96762
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KAN Query on KAN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	KANAMYCIN A C₁₈ H₃₆ N₄ O₁₁ SBUJHOSQTJFQJX-NOAMYHISSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.171 (Depositor), 0.171 (DCC)
R-Value Work: 0.146 (Depositor), 0.147 (DCC)
R-Value Observed: 0.147 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-27

Deposition Author(s):

Smith, C.A.

Vakulenko, S.B.

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

Revision History (Full details and data files)

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