4X6T | pdb_00004x6t

M.tuberculosis betalactamase complexed with inhibitor EC19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.202 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4X6T

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Inhibiting the beta-Lactamase of Mycobacterium tuberculosis (Mtb) with Novel Boronic Acid Transition-State Inhibitors (BATSIs).

Kurz, S.G.Hazra, S.Bethel, C.R.Romagnoli, C.Caselli, E.Prati, F.Blanchard, J.S.Bonomo, R.A.

(2015) ACS Infect Dis 1: 234-242

  • DOI: https://doi.org/10.1021/acsinfecdis.5b00003
  • Primary Citation Related Structures: 
    4X6T

  • PubMed Abstract: 

    BlaC, the single chromosomally encoded β-lactamase of Mycobacterium tuberculosis, has been identified as a promising target for novel therapies that rely upon β-lactamase inhibition. Boronic acid transition-state inhibitors (BATSIs) are a class of β-lactamase inhibitors which permit rational inhibitor design by combinations of various R1 and R2 side chains. To explore the structural determinants of effective inhibition, we screened a panel of 25 BATSIs to explore key structure-function relationships. We identified a cefoperazone analogue, EC19, which displayed slow, time-dependent inhibition against BlaC with a potency similar to that of clavulanate (Ki* of 0.65 ± 0.05 μM). To further characterize the molecular basis of inhibition, we solved the crystallographic structure of the EC19-BlaC(N172A) complex and expanded our analysis to variant enzymes. The results of this structure-function analysis encourage the design of a novel class of β-lactamase inhibitors, BATSIs, to be used against Mycobacterium tuberculosis.


  • Organizational Affiliation
    • Department of Medicine, Tufts Medical Center , 600 Washington Street, No. 257, Boston, Massachusetts 02111, United States.

Macromolecule Content 

  • Total Structure Weight: 29.32 kDa 
  • Atom Count: 2,341 
  • Modeled Residue Count: 265 
  • Deposited Residue Count: 265 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase265Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: blaCblaARv2068cMTCY49.07c
EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKD3 
Go to UniProtKB:  P9WKD3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKD3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3Y6

Query on 3Y6



Download:Ideal Coordinates CCD File
I [auth A]3-[(2R)-2-(dihydroxyboranyl)-2-{[(2R)-2-{[(4-ethyl-2,3-dioxo-3,4-dihydropyrazin-1(2H)-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}ethyl]benzoic acid
C24 H25 B N4 O9
ALFFAZKBOABSLT-RBUKOAKNSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.202 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.264α = 90
b = 71.417β = 90
c = 84.683γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2015-12-23 
  • Deposition Author(s): Hazra, S.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2023-09-27
    Changes: Data collection, Refinement description