7Q1D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8I8Click on this verticalbar to view details

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N(3)-acetyltransferase III
A, B, C, D
287Pseudomonas aeruginosaMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29808
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8I8 (Subject of Investigation/LOI)
Query on 8I8

Download Ideal Coordinates CCD File 
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
BTB
Query on BTB

Download Ideal Coordinates CCD File 
K [auth B]2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
M [auth C],
N [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.957α = 90
b = 100.489β = 90
c = 131.908γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8I8Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union694610
H2020 Marie Curie Actions of the European CommissionEuropean Union713482

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description