6TBJ | pdb_00006tbj

Structure of a beta galactosidase with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.145 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6TBJ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Mechanistic Insights into the Chaperoning of Human Lysosomal-Galactosidase Activity: Highly Functionalized Aminocyclopentanes and C -5a-Substituted Derivatives of 4- epi -Isofagomine.

Weber, P.Thonhofer, M.Averill, S.Davies, G.J.Santana, A.G.Muller, P.Nasseri, S.A.Offen, W.A.Pabst, B.M.Paschke, E.Schalli, M.Torvisco, A.Tschernutter, M.Tysoe, C.Windischhofer, W.Withers, S.G.Wolfsgruber, A.Wrodnigg, T.M.Stutz, A.E.

(2020) Molecules 25

  • DOI: https://doi.org/10.3390/molecules25174025
  • Primary Citation Related Structures: 
    6TBF, 6TBG, 6TBH, 6TBI, 6TBJ, 6TBK

  • PubMed Abstract: 

    Glycosidase inhibitors have shown great potential as pharmacological chaperones for lysosomal storage diseases. In light of this, a series of new cyclopentanoid β-galactosidase inhibitors were prepared and their inhibitory and pharmacological chaperoning activities determined and compared with those of lipophilic analogs of the potent β-d-galactosidase inhibitor 4- epi -isofagomine. Structure-activity relationships were investigated by X-ray crystallography as well as by alterations in the cyclopentane moiety such as deoxygenation and replacement by fluorine of a "strategic" hydroxyl group. New compounds have revealed highly promising activities with a range of β-galactosidase-compromised human cell lines and may serve as leads towards new pharmacological chaperones for G M1 -gangliosidosis and Morquio B disease.


  • Organizational Affiliation
    • Glycogroup, Institute of Chemistry and Technology of Biobased Systems, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria.

Macromolecule Content 

  • Total Structure Weight: 501.47 kDa 
  • Atom Count: 35,492 
  • Modeled Residue Count: 4,224 
  • Deposited Residue Count: 4,400 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-galactosidase, putative, bgl35A
A, B, C, D, E
A, B, C, D, E, F, G, H
550Cellvibrio japonicus Ueda107Mutation(s): 0 
Gene Names: bgl35ACJA_2707
EC: 3.2.1.23
UniProt
Find proteins for B3PBE0 (Cellvibrio japonicus (strain Ueda107))
Explore B3PBE0 
Go to UniProtKB:  B3PBE0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3PBE0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N0W
(Subject of Investigation/LOI)

Query on N0W



Download:Ideal Coordinates CCD File
CA [auth E]
HA [auth F]
L [auth A]
LA [auth G]
N [auth B]
CA [auth E],
HA [auth F],
L [auth A],
LA [auth G],
N [auth B],
QA [auth H],
R [auth C],
X [auth D]
5-(dimethylamino)-~{N}-[6-[(2~{S},3~{R},4~{S},5~{R})-3-(hydroxymethyl)-4,5-bis(oxidanyl)piperidin-2-yl]hexyl]naphthalene-1-sulfonamide
C24 H37 N3 O5 S
YUUSOYGEJQMOTK-QRVLJTFESA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth E]
DA [auth F]
EA [auth F]
FA [auth F]
AA [auth E],
BA [auth E],
DA [auth F],
EA [auth F],
FA [auth F],
GA [auth F],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
KA [auth G],
M [auth B],
MA [auth H],
NA [auth H],
O [auth C],
OA [auth H],
P [auth C],
PA [auth H],
Q [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
Y [auth E],
Z [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.145 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.416α = 89.93
b = 115.786β = 90.08
c = 116.186γ = 89.99
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/R001162/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description