2J79

BETA-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH GALACTO-HYDROXIMOLACTAM

Structural Biology Knowledgebase: 2J79 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.186

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2J79

Classification: HYDROLASE

Total Structure Weight: 108366.06

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

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

A, B (2E,3R,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)- 2-PIPERIDINONE
5-LACTAM, (Synonym)
C6 H12 N2 O5
VBXHGXTYZGYTQG-MGCNEYSASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
GTL N/A in BindingDB
Ki: 640 nM  BindingMOAD
Kd: 1100 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.186
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.16 α = 90.00
b = 94.44 β = 90.00
c = 113.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-10-06
  • Released Date: 2006-10-18
  • Deposition author(s): Gloster, T.M., Zechel, D., Vasella, A., Davies, G.J.

Revision History

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