4JFS

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

Structural Biology Knowledgebase: 4JFS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.157

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JFS

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 105697.65

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

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EPE
Query on EPE

B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
16Z
Query on 16Z

A, B (2S,3S,4R,5S)-2-(4-methoxyphenyl)-1,5-dimethylpyrrolidine- 3,4-diol
4-epi-(+)-Codonopsinine (Synonym)
C13 H19 N O3
GJZNAEFHIYPPEM-KNDHEWATSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

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

A, B IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
16Z N/A in BindingDB
Ki: 5400 nM  BindingMOAD
Ki: 5400 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.157
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 68.43 α = 90.00
b = 95.77 β = 90.81
c = 97.11 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