5CHM | pdb_00005chm

CRYSTAL STRUCTURE OF Fox-4 cephamycinase complexed with ceftazidime BATSI (LP06)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.229 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structures of FOX-4 Cephamycinase in Complex with Transition-State Analog Inhibitors.

Lefurgy, S.T.Caselli, E.Taracila, M.A.Malashkevich, V.N.Biju, B.Papp-Wallace, K.M.Bonanno, J.B.Prati, F.Almo, S.C.Bonomo, R.A.

(2020) Biomolecules 10

  • DOI: https://doi.org/10.3390/biom10050671
  • Primary Citation Related Structures: 
    5CHJ, 5CHM

  • PubMed Abstract: 

    Boronic acid transition-state analog inhibitors (BATSIs) are partners with β-lactam antibiotics for the treatment of complex bacterial infections. Herein, microbiological, biochemical, and structural findings on four BATSIs with the FOX-4 cephamycinase, a class C β-lactamase that rapidly hydrolyzes cefoxitin, are revealed. FOX-4 is an extended-spectrum class C cephalosporinase that demonstrates conformational flexibility when complexed with certain ligands. Like other β-lactamases of this class, studies on FOX-4 reveal important insights into structure-activity relationships. We show that SM23, a BATSI, shows both remarkable flexibility and affinity, binding similarly to other β-lactamases, yet retaining an IC 50 value < 0.1 μM. Our analyses open up new opportunities for the design of novel transition-state analogs of class C enzymes.


  • Organizational Affiliation
    • Department of Chemistry, Hofstra University, Hempstead, NY 11549, USA.

Macromolecule Content 

  • Total Structure Weight: 39.55 kDa 
  • Atom Count: 2,962 
  • Modeled Residue Count: 355 
  • Deposited Residue Count: 362 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase362Escherichia coliMutation(s): 0 
Gene Names: fox-4
EC: 3.5.2.6
UniProt
Find proteins for Q9L387 (Escherichia coli)
Explore Q9L387 
Go to UniProtKB:  Q9L387
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L387
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CB4

Query on CB4



Download:Ideal Coordinates CCD File
B [auth A]PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE
C10 H15 B N4 O6 S
ZECCQELUYUPTSB-UUASQNMZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
I [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.229 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.803α = 90
b = 57.144β = 95.98
c = 56.123γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary