1KC3

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.191

Literature

Macromolecules
Sequence Display for 1KC3

Classification: OXIDOREDUCTASE

Total Structure Weight: 33908.00

Macromolecule Entities
Molecule Chains Length Organism Details
dTDP-glucose oxidoreductase A 299 Salmonella enterica EC#: 1.1.1.133 IUBMB
Gene Name(s): rfbD rmlD STM2096
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRH
Query on TRH

A 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
C16 H26 N2 O15 P2
ZOSQFDVXNQFKBY-CGAXJHMRSA-N
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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.191
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 47.98 α = 90.00
b = 72.26 β = 90.00
c = 82.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-07
  • Released Date: 2002-06-28
  • Deposition author(s): Blankenfeldt, W., Kerr, I.D., Giraud, M.F., McMiken, H.J., Leonard, G.A., Whitfield, C., Messner, P., Graninger, M., Naismith, J.H.

Revision History

  • Version 1_0: 2002-06-28

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance