2JKE

STRUCTURE OF A FAMILY 97 ALPHA-GLUCOSIDASE FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH DEOXYNOJIRIMYCIN

Structural Biology Knowledgebase: 2JKE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.155

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2JKE

Classification: HYDROLASE

Total Structure Weight: 167518.97

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-GLUCOSIDASE (ALPHA-GLUCOSIDASE SUSB) A, B 727 Bacteroides thetaiotaomicron EC#: 3.2.1.3 IUBMB
Fragment: RESIDUES 22-738
Gene Name(s): susB BT_3703

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

A, B 1-DEOXYNOJIRIMYCIN
MORANOLINE (Synonym)
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NOJ N/A in BindingDB
Ki: 59000 nM  BindingMOAD
Ki: 59000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.155
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.72 α = 90.00
b = 112.24 β = 100.86
c = 102.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-08-28
  • Released Date: 2008-09-30
  • Deposition author(s): Gloster, T.M., Turkenburg, J.P., Potts, J.R., Henrissat, B., Davies, G.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4