7UUL | pdb_00007uul

Crystal structure of aminoglycoside resistance enzyme ApmA, complex with kanamycin B and coenzyme A

PDB DOI: https://doi.org/10.2210/pdb7UUL/pdb

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

Deposited: 2022-04-28 Released: 2022-11-02
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Bordeleau, E., Wright, G.D., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID), 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: 2.26 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (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 1.5 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: 196.21 kDa
Atom Count: 15,641
Modeled Residue Count: 1,648
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminocyclitol acetyltransferase ApmA	A, B, C, D, E A, B, C, D, E, F	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1D0AST6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain H [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain H [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain H [auth A]	AA [auth D], FA [auth E], H [auth A], M [auth B], T [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C]
9CS (Subject of Investigation/LOI) Query on 9CS Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain Z [auth D] SDF format, chain S [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain S [auth C] mmCIF format, chain EA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain S [auth C]	EA [auth E] G [auth A] L [auth B] R [auth C] S [auth C] EA [auth E], G [auth A], L [auth B], R [auth C], S [auth C], Z [auth D]	(1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE C₁₈ H₃₇ N₅ O₁₀ SKKLOUVUUNMCJE-FQSMHNGLSA-N		Interactions Focus chain EA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth D] Interactions & Density Focus chain EA [auth E] Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain Z [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain HA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth C] SDF format, chain KA [auth F] MOL2 format, chain CA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain KA [auth F] mmCIF format, chain CA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain KA [auth F]	CA [auth D] HA [auth E] J [auth A] K [auth A] KA [auth F] CA [auth D], HA [auth E], J [auth A], K [auth A], KA [auth F], O [auth B], P [auth B], Q [auth B], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth D] Focus chain HA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain HA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain JA [auth F] SDF format, chain IA [auth F] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain JA [auth F] MOL2 format, chain IA [auth F] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain JA [auth F] mmCIF format, chain IA [auth F]	BA [auth D] GA [auth E] I [auth A] IA [auth F] JA [auth F] BA [auth D], GA [auth E], I [auth A], IA [auth F], JA [auth F], N [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain JA [auth F] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] MOL2 format, chain DA [auth D] mmCIF format, chain DA [auth D]	DA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Interactions & Density Focus chain DA [auth D]