4JFV

Crystal structure of a bacterial fucosidase with iminosugar inhibitor (2S,3S,4R,5S)-2-[N-(methylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol

Structural Biology Knowledgebase: 4JFV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JFV

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 210999.29

Macromolecule Entities
Molecule Chains Length Organism Details
alpha-L-fucosidase A, B, C, D 450 Bacteroides thetaiotaomicron Fragment: RESIDUES 35-484
Gene Name(s): BT_2970

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
H57
Query on H57

A, B, C, D (3alpha)-[({2-[(2S,3S,4R,5S)-3,4-dihydroxy- 5-methylpyrrolidin-2-yl]ethyl}amino)methyl]ferrocene
3S, (Synonym)
C18 H26 Fe N2 O2
ZWSGRBUXVKPKCO-IMFJELSCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A, B, C, D IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
H57 N/A in BindingDB
Ki: 520 nM  BindingMOAD
Ki: 520 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.190
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 55.54 α = 90.00
b = 187.00 β = 94.19
c = 97.67 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

  • 2014-07-02
    Type: Non-polymer description | Details: --