1KEW

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with thymidine diphosphate bound

Structural Biology Knowledgebase: 1KEW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 1KEW

Classification: LYASE

Total Structure Weight: 83943.34

Macromolecule Entities
Molecule Chains Length Organism Details
dTDP-D-glucose 4,6-dehydratase A, B 361 Salmonella enterica EC#: 4.2.1.46 IUBMB
Gene Name(s): rfbB STM2097
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TYD
Query on TYD

A, B THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.205
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 169.90 α = 90.00
b = 169.90 β = 90.00
c = 92.83 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-17
  • Released Date: 2002-01-25
  • Deposition author(s): Allard, S.T.M., Beis, K., Giraud, M.-F., Hegeman, A.D., Gross, J.W., Whitfield, C., Graninger, M., Messner, P., Allen, A.G., Naismith, J.H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update