4FNS

Crystal structure of GH36 alpha-galactosidase AgaA A355E from Geobacillus stearothermophilus in complex with 1-deoxygalactonojirimycin

Structural Biology Knowledgebase: 4FNS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.174

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4FNS

Classification: Hydrolase

Total Structure Weight: 334685.69

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-galactosidase AgaA A, B, C, D 729 Geobacillus stearothermophilus EC#: 3.2.1.22 IUBMB
Mutation: A355E, F518L, M704V
Gene Name(s): agaA

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

A, B, C, D (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine- 3,4,5-triol
1-deoxygalactonojirimycin (Synonym)
C6 H13 N O4
LXBIFEVIBLOUGU-DPYQTVNSSA-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)
EDO
Query on EDO

D 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DGJ N/A in BindingDB
N/A in BindingMoad
Ki: 200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.174
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 150.30 α = 90.00
b = 150.30 β = 90.00
c = 233.36 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-06-20
  • Released Date: 2012-10-03
  • Deposition author(s): Merceron, R., Foucault, M., Haser, R., Mattes, R., Watzlawick, H., Gouet, P.

Revision History

  • 2013-02-20
    Type: Citation | Details: Citation update