7Q0Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Models: experimental
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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 8I5Click on this verticalbar to view details

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminoglycoside N(3)-acetyltransferase III
A, B
269Pseudomonas 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
8I5 (Subject of Investigation/LOI)
Query on 8I5

Download Ideal Coordinates CCD File 
E [auth A]3N methyl nemycin B
C24 H48 N6 O13
FCJYTWXMZQXWFB-HGRVKHENSA-N
PEG
Query on PEG

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H [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

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C [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.59α = 90
b = 89.235β = 90
c = 103.248γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
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 8I5Click 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