8PXZ

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with natural substrate

• PDB DOI: https://doi.org/10.2210/pdb8PXZ/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-24 Released: 2024-08-07 
• Deposition Author(s): de Munnik, M., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with natural substrate

de Munnik, M., Schofield, C.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 38.89 kDa 
• Atom Count: 3,069 
• Modelled Residue Count: 351 
• Deposited Residue Count: 355 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L,D-transpeptidase 2	A	355	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: ldtB, MT2594, V735_02606 EC: 2.3.2
UniProt
Find proteins for O53223 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore O53223  Go to UniProtKB:  O53223

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I36 (Subject of Investigation/LOI)	E [auth A]	(2~{R})-2-[[(2~{S},6~{R})-6,7-bis(azanyl)-2-[[(4~{R})-4,5-bis(azanyl)-5-oxidanylidene-pentanoyl]amino]-7-oxidanylidene-heptanoyl]amino]propanoic acid C15 H28 N6 O6 CJJCRMCFCZMAJA-KYXWUPHJSA-N
I1V (Subject of Investigation/LOI)	B [auth A]	(2~{R})-2-azanyl-~{N}'-[(2~{S},6~{R})-6,7-bis(azanyl)-1-oxidanyl-7-oxidanylidene-heptan-2-yl]pentanediamide C12 H25 N5 O4 JJMJHAUQDTZOGG-DJLDLDEBSA-N
DAL	D [auth A]	D-ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-UWTATZPHSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.226 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.12	α = 90
b = 95.83	β = 90
c = 59.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): de Munnik, M., Schofield, C.J.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release