6RRM

Crystal structure of LdtMt2 from Mycobacterium tuberculosis bound to Ebselen

• PDB DOI: https://doi.org/10.2210/pdb6RRM/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Mycobacterium tuberculosis CDC1551
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-20 Released: 2019-08-14 
• Deposition Author(s): Brem, J., Lohans, C., Schofield, C.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Targeting the Mycobacterium tuberculosis transpeptidase LdtMt2with cysteine-reactive inhibitors including ebselen.

de Munnik, M., Lohans, C.T., Lang, P.A., Langley, G.W., Malla, T.R., Tumber, A., Schofield, C.J., Brem, J.

(2019) Chem Commun (Camb) 55: 10214-10217

• PubMed: 31380528 
• DOI: https://doi.org/10.1039/c9cc04145a
• Primary Citation of Related Structures:  
  6RLG, 6RRM


• PubMed Abstract: 
  

  The l,d-transpeptidases (Ldts) are promising antibiotic targets for treating tuberculosis. We report screening of cysteine-reactive inhibitors against LdtMt2 from Mycobacterium tuberculosis. Structural studies on LdtMt2 with potent inhibitor ebselen reveal opening of the benzisoselenazolone ring by a nucleophilic cysteine, forming a complex involving extensive hydrophobic interactions with a substrate-binding loop.

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Organizational Affiliation: 

Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.85 kDa 
• Atom Count: 5,942 
• Modelled Residue Count: 702 
• Deposited Residue Count: 710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A, B	355	Mycobacterium tuberculosis CDC1551	Mutation(s): 0  Gene Names: ldtB, MT2594, V735_02606 EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2  Go to UniProtKB:  I6Y9J2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9JT (Subject of Investigation/LOI)	F [auth A], I [auth B]	N-phenyl-2-selanylbenzamide C13 H11 N O Se PVPUYGNPKBMXGO-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	G [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NH4	C [auth A], E [auth A], H [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.223 
• R-Value Work: 0.200 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.22	α = 90
b = 93.57	β = 93.01
c = 75.49	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Brem, J., Lohans, C., Schofield, C.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Derived calculations
• Version 1.2: 2019-09-04
  Changes: Data collection, Database references
• Version 1.3: 2023-04-12
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary