2WBG

Structure of family 1 beta-glucosidase from Thermotoga maritima in complex with 3-imino-2-oxa-(+)-castanospermine

Structural Biology Knowledgebase: 2WBG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2WBG

Classification: HYDROLASE

Total Structure Weight: 217089.83

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-GLUCOSIDASE A A, B, C, D 468 Thermotoga maritima EC#: 3.2.1.21 IUBMB
Fragment: RESIDUES 2-446
Gene Name(s): bglA

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

A, B, C, D (3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4- a]pyridine-5,6,7,8-tetrol
C15 H28 N2 O5
QJILQIWQVOAQBB-KRIYVDMXSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

C ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LGS N/A in BindingDB
Ki: 35200 nM  BindingMOAD
Ki: 35200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.153
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.99 α = 90.00
b = 73.19 β = 94.03
c = 138.09 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-02-27
  • Released Date: 2009-04-14
  • Deposition author(s): Aguilar, M., Gloster, T.M., Turkenburg, J.P., Garcia-Moreno, M.I., Ortiz Mellet, C., Davies, G.J., Garcia Fernandez, J.M.

Revision History

  • 2012-08-01
    Type: Refinement description | Details: REMARK 3
  • 2012-08-01
    Type: Non-polymer description | Details: FORMUL,HETSYN
  • 2012-08-01
    Type: Other | Details: REMARK 525
  • 2012-08-01
    Type: Geometry validation | Details: REMARK 500
  • 2012-08-01
    Type: Citation | Details: JRNL
  • 2012-08-01
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2012-08-01
    Type: Version format compliance | Details: REMARK 4