4QR7 | pdb_00004qr7

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.268 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MLDClick on this verticalbar to view detailsBest fitted DWZClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history. 


Literature

Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation

Gokulan, K., Khare, S., Cerniglia, C.E., Foley, S.L., Varughese, K.I.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L,d-transpeptidase LdtB352Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ldtB, Rv2518c, RVBD_2518c
EC: 2.3.2
UniProt
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6Y9J2 
Go to UniProtKB:  I6Y9J2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6Y9J2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLD
Query on MLD
Download Ideal Coordinates CCD File 
B [auth A]GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA
C37 H59 N7 O20
UPFMKPIBAIPLHT-RSJSDIDPSA-N
DWZ
Query on DWZ
Download Ideal Coordinates CCD File 
C [auth A](2S,3R,4S)-4-{[(3S,5S)-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-VGWSNGFZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.33α = 90
b = 66.459β = 90
c = 206.865γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
Auto-Rickshawphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MLDClick on this verticalbar to view detailsBest fitted DWZClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2022-02-02
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Data collection, Structure summary