3FSX

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 3FSX

Classification: TRANSFERASE

Total Structure Weight: 172829.03

Macromolecule Entities
Molecule Chains Length Organism Details
Tetrahydrodipicolinate N-succinyltransferase A, B, C, D, E 332 Mycobacterium tuberculosis EC#: 2.3.1.117 IUBMB
Gene Name(s): dapD Rv1201c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, D (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A, B, C, D ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, D, E SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.168
  • Space Group: I 21 3

Unit Cell:

Length (Å) Angle (°)
a = 216.99 α = 90.00
b = 216.99 β = 90.00
c = 216.99 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-01-12
  • Released Date: 2009-06-23
  • Deposition author(s): Schuldt, L., Weyand, S., Kefala, G., Weiss, M.S.

Revision History

  • 2011-07-13
    Type: Advisory, Version format compliance