4EBP

BlaC E166A Cefotaxime Acyl-Intermediate Complex

• PDB DOI: https://doi.org/10.2210/pdb4EBP/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: 2.29 Å
• R-Value Free: 0.240 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Starting Model: experimental

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: 114.51 kDa 
• Atom Count: 7,948 
• Modelled Residue Count: 1,046 
• 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
CEF	I [auth B], K [auth C]	CEFOTAXIME, C3' cleaved, open, bound form C14 H15 N5 O5 S2 NRYMPLKBKFIWQC-YVCCLBOHSA-N
PO4	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], L [auth C], M [auth D], N [auth D], O [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.240 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.82	α = 90
b = 96.152	β = 106.34
c = 107.088	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	refinement
DENZO	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 2.0: 2018-09-19
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary