4EBL | pdb_00004ebl

BlaC E166A Faropenem Acyl-Intermediate Complex

• PDB DOI: https://doi.org/10.2210/pdb4EBL/pdb

• Classification: Hydrolase/Antibiotic
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-03-23 Released: 2013-04-03 
• Deposition Author(s): Mire, J.A., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.204 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Faropenem is Effective Against Mycobacterium tuberculosis in vitro and in vivo

Mire, J.A., Pai, P., Siddiqi, N., Russell, D.H., Rubin, E.J., Sacchettini, J.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 114.19 kDa 
• Atom Count: 8,380 
• Modeled Residue Count: 1,060 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	265	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: blaA, blaC, MT2128, MTCY49.07c, Rv2068c EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD3  Go to UniProtKB:  P9WKD3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGF	I [auth B], L [auth C]	(2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid C12 H17 N O5 S FHQOUTNMKXYVEY-MKSGQPMJSA-N
PO4	E [auth A], F [auth A], G [auth A], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.204 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.792	α = 90
b = 96.946	β = 107.95
c = 109.526	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Mire, J.A., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Non-polymer description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary