9LTK | pdb_00009ltk

Crystal structur of Lpg1618(R215F) from Legionella pneumophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.187 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structural and molecular characterization of AmpS, a class D beta-lactamase from Legionella pneumophila.

Gao, J.Liu, T.Lu, L.Zhou, Z.Sun, W.Chen, Y.Xu, W.Wang, N.Ma, J.Ge, H.

(2025) Int J Biol Macromol 312: 144174-144174

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.144174
  • Primary Citation of Related Structures:  
    9LTK

  • PubMed Abstract: 

    In Gram-negative bacteria, β-lactamase enzymes represent one of the most prevalent mechanisms of antibiotic resistance. These enzymes confer resistance by hydrolyzing the four-membered β-lactam ring in β-lactam antibiotics, resulting in inactive derivatives. In this study, we report the 1.9 Å crystal structure of the R215F mutant of AmpS, a class D β-lactamase OXA-29 from Legionella pneumophila. The R215F mutation was designed to mimic the phenylalanine residue present at the equivalent position in E. coli OXA-1, thereby enabling functional investigation of the surrounding region and its role in substrate specificity. Through molecular docking simulations, enzymatic activity assays, and physiological analyses, we characterized the molecular properties of AmpS and its contribution to β-lactam resistance in L. pneumophila. Our findings provide new insights into the function of AmpS, underscoring its contribution to antibiotic resistance and offering a foundation for the development of therapeutic strategies aimed at mitigating β-lactamase-mediated resistance in pathogenic bacteria such as L. pneumophila.


  • Organizational Affiliation
    • Institute of Health Sciences and Technology, Institutes of Physical Sciences and Information Technology, Anhui University, Hefei, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
253Legionella pneumophilaMutation(s): 1 
Gene Names: lpg1618
EC: 3.5.2.6
UniProt
Find proteins for A0AAN5PFI7 (Legionella pneumophila)
Explore A0AAN5PFI7 
Go to UniProtKB:  A0AAN5PFI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAN5PFI7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.187 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.189α = 90
b = 156.189β = 90
c = 156.189γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPXdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32370196

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release