5D7H

X-RAY CRYSTAL STRUCTURE OF L,D TRANSPEPTIDASE 2 FROM MYCOBACTERIUM TUBERCULOSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase LdtMt2 by biapenem and tebipenem.

Bianchet, M.A.Pan, Y.H.Basta, L.A.B.Saavedra, H.Lloyd, E.P.Kumar, P.Mattoo, R.Townsend, C.A.Lamichhane, G.

(2017) BMC Biochem. 18: 8-8

  • DOI: 10.1186/s12858-017-0082-4
  • Primary Citation of Related Structures:  
  • Also Cited By: 6BOI

  • PubMed Abstract: 
  • The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that ge ...

    The carbapenem subclass of β-lactams is among the most potent antibiotics available today. Emerging evidence shows that, unlike other subclasses of β-lactams, carbapenems bind to and inhibit non-classical transpeptidases (L,D-transpeptidases) that generate 3 → 3 linkages in bacterial peptidoglycan. The carbapenems biapenem and tebipenem exhibit therapeutically valuable potencies against Mycobacterium tuberculosis (Mtb).


    Organizational Affiliation

    Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA.,Chemistry Department, United States Naval Academy, Annapolis, MD, 21402, USA.,Division of Infectious Diseases, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Baltimore, MD, 21231, USA. lamichhane@jhu.edu.,Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA.,Department of Chemistry, Johns Hopkins University, Baltimore, MD, 21218, USA.,Division of Infectious Diseases, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, 1503 E. Jefferson Street, Baltimore, MD, 21231, USA.,Division of Infectious Diseases, Center for Tuberculosis Research, Taskforce to study Resistance Emergence & Antimicrobial development Technology (TREAT), Johns Hopkins University School of Medicine, Baltimore, MD, 21231, USA. lamichhane@jhu.edu.,Department of Neurology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA. bianchet@jhmi.edu.,Department of Biophysics and Biophysical Chemistry, Structural Enzymology and Thermodynamics Group, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA. bianchet@jhmi.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L,D-transpeptidase 2
A, B
352Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: ldtB
EC: 2.3.2.-
Find proteins for O53223 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  O53223
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.265α = 90.00
b = 95.579β = 92.59
c = 75.550γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR21AI111739
National Institutes of Health/Office of the DirectorUnited StatesDP2OD008459

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Author supporting evidence, Database references, Derived calculations