4QTF

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: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.1 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L,d-transpeptidase LdtBA349Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ldtBRv2518cRVBD_2518clppSP425_02624
EC: 2.3.2
Find proteins for I6Y9J2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6Y9J2 
Go to UniProtKB:  I6Y9J2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
3V5
Query on 3V5

Download Ideal Coordinates CCD File 
C [auth A](3S,5S)-3-({[(aminomethyl)amino]methyl}sulfanyl)-5-[(2S)-1,3-dioxobutan-2-yl]-L-proline
C11 H19 N3 O4 S
SKDDBJCIWUNJNL-XKNYDFJKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.272α = 90
b = 65.881β = 90
c = 207.456γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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