7Q1D | pdb_00007q1d

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

PDB DOI: https://doi.org/10.2210/pdb7Q1D/pdb

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

Deposited: 2021-10-18 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: 1.43 Å
R-Value Free:
0.200 (Depositor), 0.196 (DCC)
R-Value Work:
0.176 (Depositor), 0.172 (DCC)
R-Value Observed:
0.178 (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

3-N-alkylation in aminoglycoside antibiotic neomycin B overcomes bacterial resistance mediated by acetyltransferase (3) IIIa

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: 132.21 kDa
Atom Count: 9,888
Modeled Residue Count: 1,057
Deposited Residue Count: 1,148
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, C, D	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8I8 (Subject of Investigation/LOI) Query on 8I8 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D]	H [auth A], L [auth B], O [auth C], Q [auth D]	[[(2~{R},3~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[(3~{S})-3-[2-[(1~{S})-1-[[(1~{S},2~{R},3~{R},4~{S},5~{R})-5-azanyl-3-[(4~{S},5~{R})-4-[(2~{S},3~{R},4~{R},5~{S},6~{E})-3-azanyl-6-(azanylmethylidene)-4,5-bis(oxidanyl)oxan-2-yl]oxy-5-(hydroxymethyl)-3-oxidanyl-oxolan-2-yl]oxy-2-[(2~{S},3~{R},4~{R},5~{S})-3-azanyl-6-(iminomethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-4-oxidanyl-cyclohexyl]amino]-1-oxidanyl-ethyl]sulfanylethylamino]-3-oxidanyl-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate C₄₆ H₈₂ N₁₃ O₃₀ P₃ S KNUGXPWVQDBKDV-VYRIPBRXSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain Q [auth D]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	I [auth A], J [auth B], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]