3THD

Crystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin

Structural Biology Knowledgebase: 3THD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3THD

Classification: HYDROLASE

Total Structure Weight: 300263.28

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-galactosidase A, B, C, D 654 Homo sapiens EC#: 3.2.1.23 IUBMB
Gene Name(s): GLB1 Gene View ELNR1

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

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

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

A, B, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DGJ IC50: 90000 nM (100) BindingDB

N/A in BindingMoad
IC50: 90000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.198
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.79 α = 90.00
b = 116.00 β = 92.22
c = 140.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-18
  • Released Date: 2011-12-07
  • Deposition author(s): Ohto, U., Shimizu, T.

Revision History

  • 2013-07-10
    Type: Citation | Details: Citation update