7Q1X | pdb_00007q1x

Acetyltrasferase(3) type IIIa in complex with neomycin B

PDB DOI: https://doi.org/10.2210/pdb7Q1X/pdb

Classification: ANTIBIOTIC
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-10-21 Released: 2022-11-02
Deposition Author(s): Pontillo, N., Guskov, A.
Funding Organization(s): European Research Council (ERC), H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.166 (Depositor), 0.166 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The 3-N-alkylation of the neomycin B outmaneuvers the aminoglycoside resistant enzyme acetyltransferase(3)IIIa via an unexpected mechanism

Pontillo, N., Warszawik, E.M., Partipilo, M., Stetsenko, A., Loznik, M., Yang, X., Slotboom, D.J., Guskov, A., Herrmann, A.

To be published.

Macromolecule Content

Total Structure Weight: 64.59 kDa
Atom Count: 4,848
Modeled Residue Count: 531
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N(3)-acetyltransferase III	A, B	287	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: aacC3 EC: 2.3.1.81
UniProt
Find proteins for P29808 (Pseudomonas aeruginosa) Explore P29808 Go to UniProtKB: P29808
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29808
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMY (Subject of Investigation/LOI) Query on NMY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	NEOMYCIN C₂₃ H₄₆ N₆ O₁₃ PGBHMTALBVVCIT-VCIWKGPPSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B]	D [auth A], E [auth A], J [auth B], K [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth A], I [auth B], L [auth B], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth B] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	H [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]