3BM6 | pdb_00003bm6

AmpC beta-lactamase in complex with a p.carboxyphenylboronic acid

• PDB DOI: https://doi.org/10.2210/pdb3BM6/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-12 Released: 2009-02-17 
• Deposition Author(s): Tondi, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.258 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Structural study of phenyl boronic acid derivatives as AmpC beta-lactamase inhibitors.

Tondi, D., Calo, S., Shoichet, B.K., Costi, M.P.

(2010) Bioorg Med Chem Lett 20: 3416-3419

• PubMed: 20452208 
• DOI: https://doi.org/10.1016/j.bmcl.2010.04.007
• Primary Citation Related Structures: 
  3BM6


• PubMed Abstract: 
  

  A small set of boronic acids acting as low nanomolar inhibitors of AmpC beta-lactamase were designed and synthesized in the effort to improve affinity, pharmacokinetic properties, and to provide a valid lead compound. X-ray crystallography revealed the binary complex of the best inhibitor bound to the enzyme, highlighting possibilities for its further rational derivatization and chemical optimization.

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Organizational Affiliation: 
• Dipartimento di Scienze Farmaceutiche, Università degli Studi di Modena e Reggio Emilia, Via Campi 183, 41126 Modena, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 80.11 kDa 
• Atom Count: 5,921 
• Modeled Residue Count: 716 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	358	Escherichia coli	Mutation(s): 0  Gene Names: ampC, ampA EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811  Go to UniProtKB:  P00811

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C9P	C [auth A], D [auth B]	4-(dihydroxyboranyl)-2-({[4-(phenylsulfonyl)thiophen-2-yl]sulfonyl}amino)benzoic acid C17 H14 B N O8 S3 JJPKFZAOXOEFHQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.258 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.908	α = 90
b = 77.18	β = 115.98
c = 97.937	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Tondi, D.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2023-08-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary