3TUR

Crystal Structure of M. tuberculosis LD-transpeptidase type 2 complexed with a peptidoglycan fragment

Structural Biology Knowledgebase: 3TUR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3TUR

Classification: PEPTIDOGLYCAN BINDING PROTEIN

Total Structure Weight: 68902.52

Macromolecule Entities
Molecule Chains Length Organism Details
Mycobacteria Tuberculosis LD-transpeptidase type 2 A, B 287 Mycobacterium tuberculosis EC#: 2.3.2 IUBMB
Gene Name(s): ldtB MT2594 V735_02606

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0JC
Query on 0JC

A, B Di-mu-iodobis(ethylenediamine)diplatinum(II)
C4 H16 I2 N4 Pt2
XXLKNYJQAYMQHB-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PT
Query on PT

B PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
6CL
Query on 6CL

A 6-CARBOXYLYSINE
C7 H15 N2 O4
GMKMEZVLHJARHF-SYDPRGILSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DGL
Query on DGL

A D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.199
  • Space Group: I 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 119.13 α = 90.00
b = 120.83 β = 90.00
c = 122.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-17
  • Released Date: 2012-12-05
  • Deposition author(s): Bianchet, M.A., Erdemli, S.B., Gupta, R., Lamichhane, G., Amzel, L.M.

Revision History

  • 2012-12-26
    Type: Citation | Details: Citation update
  • 2012-12-12
    Type: Citation | Details: Citation update