4IIE

Crystal structure of beta-glucosidase 1 from Aspergillus aculeatus in complex with calystegine B(2)

Structural Biology Knowledgebase: 4IIE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.149

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4IIE

Classification: Hydrolase

Total Structure Weight: 199048.11

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-glucosidase 1 A, B 841 Aspergillus aculeatus EC#: 1.2.1.8 IUBMB 3.2.1.21 IUBMB
Gene Name(s):

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A, B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CGB
Query on CGB

A, B CALYSTEGINE B2
2,,2R (Synonym)
C7 H13 N O4
FXFBVZOJVHCEDO-IBISWUOJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

A, B (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CGB N/A in BindingDB
Ki: 4600000 nM  BindingMOAD
Ki: 4600000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.193
  • R-Value Work: 0.149
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.13 α = 90.00
b = 122.15 β = 90.00
c = 222.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-20
  • Released Date: 2013-04-10
  • Deposition author(s): Suzuki, K., Sumitani, J., Kawaguchi, T., Fushinobu, S.

Revision History

  • 2013-07-31
    Type: Citation | Details: Citation update