7UUJ | pdb_00007uuj

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with gentamicin

PDB DOI: https://doi.org/10.2210/pdb7UUJ/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-28 Released: 2023-04-19
Deposition Author(s): Stogios, P.J., Evdokimova, E., Osipiuk, J., Di Leo, R., Bordeleau, E., Wright, G.D., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.172 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance

Bordeleau, E., Stogios, P.J., Evdokimova, E., Koteva, K., Savchenko, A., Wright, G.D.

(2024) Nat Chem Biol 20: 234-242

DOI: https://doi.org/10.1038/s41589-023-01483-3

Macromolecule Content

Total Structure Weight: 95.65 kDa
Atom Count: 7,570
Modeled Residue Count: 821
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminocyclitol acetyltransferase ApmA	A, B, C	276	Staphylococcus aureus	Mutation(s): 0 Gene Names: apmA
UniProt
Find proteins for A0A1D0AST6 (Staphylococcus aureus) Explore A0A1D0AST6 Go to UniProtKB: A0A1D0AST6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1D0AST6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLL (Subject of Investigation/LOI) Query on LLL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B]	D [auth A], G [auth B], I [auth B]	(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL C₁₉ H₃₉ N₅ O₇ VEGXETMJINRLTH-BOZYPMBZSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth C]	E [auth A], H [auth B], K [auth C], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]