7Q0Q

Acetyltrasferase(3) type IIIa in complex with 3-N-methyl-nemycin B

PDB DOI: https://doi.org/10.2210/pdb7Q0Q/pdb

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

Deposited: 2021-10-16 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: 1.96 Å
R-Value Free: 0.236
R-Value Work: 0.190
R-Value Observed: 0.192

Starting Models: 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: 59.94 kDa
Atom Count: 4,685
Modelled Residue Count: 527
Deposited Residue Count: 538
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside N(3)-acetyltransferase III	A, B	269	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29808
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8I5 (Subject of Investigation/LOI) Query on 8I5 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]	3N methyl nemycin B C₂₄ H₄₈ N₆ O₁₃ FCJYTWXMZQXWFB-HGRVKHENSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A]	C [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain F [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	G [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]