1P9L

Structure of M. tuberculosis dihydrodipicolinate reductase in complex with NADH and 2,6 PDC

Structural Biology Knowledgebase: 1P9L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1P9L

Classification: OXIDOREDUCTASE

Total Structure Weight: 53446.49

Macromolecule Entities
Molecule Chains Length Organism Details
dihydrodipicolinate reductase A, B 245 Mycobacterium tuberculosis EC#: 1.17.1.8 IUBMB
Gene Name(s): dapB Rv2773c MTV002.38c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH (Synonym)
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG4
Query on PG4

B TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PDC
Query on PDC

A, B PYRIDINE-2,6-DICARBOXYLIC ACID
DIPICOLINIC ACID (Synonym)
C7 H5 N O4
WJJMNDUMQPNECX-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.193
  • Space Group: I 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.29 α = 90.00
b = 117.28 β = 90.00
c = 78.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-12
  • Released Date: 2003-08-26
  • Deposition author(s): Cirilli, M., Zheng, R., Scapin, G., Blanchard, J.S., TB Structural Genomics Consortium (TBSGC)

Revision History

  • 2013-11-06
    Type: Non-polymer description | Details: relabeled ligand NAD as NAI
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values