3VYP

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2-N140 adduct with meropenem

• PDB DOI: https://doi.org/10.2210/pdb3VYP/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-30 Released: 2013-06-19 
• Deposition Author(s): Li, W.J., Li, D.F., Bi, L.J., Wang, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

Crystal structure of L,D-transpeptidase LdtMt2 in complex with meropenem reveals the mechanism of carbapenem against Mycobacterium tuberculosis

Li, W.J., Li, D.F., Hu, Y.L., Zhang, X.E., Bi, L.J., Wang, D.C.

(2013) Cell Res 23: 728-731

• PubMed: 23588382 
• DOI: https://doi.org/10.1038/cr.2013.53
• Primary Citation of Related Structures:  
  3VYN, 3VYO, 3VYP

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.

Macromolecule Content

• Total Structure Weight: 59.52 kDa 
• Atom Count: 5,076 
• Modelled Residue Count: 532 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable conserved lipoprotein LPPS	A, B	269	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv2518c EC: 2.3.2.12 (PDB Primary Data), 2.3.2 (UniProt)
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y9J2  Go to UniProtKB:  I6Y9J2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MXR	D [auth A], F [auth B]	(2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid C17 H27 N3 O5 S UUIYVKJXUXGPKB-DKLFCYGSSA-N
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.61	α = 90
b = 73.28	β = 90
c = 103.63	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Li, W.J., Li, D.F., Bi, L.J., Wang, D.C.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary