1VS0

Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 1VS0

Classification: LIGASE

Total Structure Weight: 69898.51

Macromolecule Entities
Molecule Chains Length Organism Details
Putative DNA ligase-like protein Rv0938/MT0965 A, B 310 Mycobacterium tuberculosis Fragment: LigD ligase domain
Mutation: M461M, K481X, M545M, M665M, M694M
Details: Adenylated form
Gene Name(s): ligD Rv0938 MTCY08D9.01c MTCY10D7.36c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET
APK
Query on APK
A, B L-PEPTIDE LINKING C16 H26 N7 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.192
  • Space Group: P 32 2 1

Unit Cell:

Length (Å) Angle (°)
a = 57.10 α = 90.00
b = 57.10 β = 90.00
c = 368.96 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-01-27
  • Released Date: 2006-02-28
  • Deposition author(s): Akey, D., Martins, A., Aniukwu, J., Glickman, M.S., Shuman, S., Berger, J.M., TB Structural Genomics Consortium (TBSGC)

Revision History

  • Version 1_0: 2006-02-28

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Advisory, Source and taxonomy, Version format compliance