4JFT

Crystal structure of a bacterial fucosidase with iminosugar inhibitor N-desmethyl-4-epi-(+)-Codonopsinine

Structural Biology Knowledgebase: 4JFT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 4JFT

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 105868.78

Macromolecule Entities
Molecule Chains Length Organism Details
alpha-L-fucosidase A, B 450 Bacteroides thetaiotaomicron Fragment: RESIDUES 35-484
Gene Name(s): BT_2970
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1KN
Query on 1KN

A, B (2S,3S,4R,5S)-2-(4-methoxyphenyl)-5-methylpyrrolidine- 3,4-diol
N-desmethyl-4-epi-(+)-Codonopsinine (Synonym)
C12 H17 N O3
RMKWLQBEDHKISQ-VKZDFBPFSA-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)
GOL
Query on GOL

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

A, B IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1KN N/A in BindingDB
Ki: 3500 nM  BindingMOAD
Ki: 3500 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.181
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 67.50 α = 90.00
b = 94.65 β = 90.87
c = 96.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-28
  • Released Date: 2013-09-18
  • Deposition author(s): Wright, D.W., Davies, G.J.

Revision History

No revisions since initial release