1KEP

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound

Structural Biology Knowledgebase: 1KEP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.172
  • R-Value Work: 0.145

Literature

Macromolecules
Sequence Display for 1KEP

Classification: LYASE

Total Structure Weight: 80648.98

Macromolecule Entities
Molecule Chains Length Organism Details
dTDP-D-glucose 4,6-dehydratase A, B 348 Streptococcus suis EC#: 4.2.1.46 IUBMB
Gene Name(s): rmlB SMU_1457
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)
TDX
Query on TDX

A, B THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
C15 H24 N2 O15 P2
AJUADKZRQSBUAK-KDGZBOQCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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: 0.172
  • R-Value Work: 0.145
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 62.45 α = 90.00
b = 97.18 β = 90.00
c = 185.47 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-16
  • 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

  • 2017-02-01
    Type: Entry authorship | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4