1UZ4 | pdb_00001uz4

Common inhibition of beta-glucosidase and beta-mannosidase by isofagomine lactam reflects different conformational intineraries for glucoside and mannoside hydrolysis

• PDB DOI: https://doi.org/10.2210/pdb1UZ4/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio mixtus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-03-04 Released: 2004-11-03 
• Deposition Author(s): Vincent, F., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.165 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.133 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Common Inhibition of Both Beta-Glucosidases and Beta-Mannosidases by Isofagomine Lactam Reflects Different Conformational Itineraries for Pyranoside Hydrolysis

Vincent, F., Gloster, T.M., Macdonald, J., Morland, C., Stick, R.V., Dias, F., Prates, J., Fontes, C.M.G.A., Gilbert, H.J., Davies, G.J.

(2004) Chembiochem 5: 1596

• PubMed: 15515081 
• DOI: https://doi.org/10.1002/cbic.200400169
• Primary Citation Related Structures: 
  1UZ1, 1UZ4

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Organizational Affiliation: 
• Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5YW, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 50.76 kDa 
• Atom Count: 3,870 
• Modeled Residue Count: 410 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAN5A	A	440	Cellvibrio mixtus	Mutation(s): 0  EC: 3.2.1.78
UniProt
Find proteins for Q6QT42 (Cellvibrio mixtus) Explore Q6QT42  Go to UniProtKB:  Q6QT42

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IFL	B [auth A]	(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE C6 H11 N O4 ARBXEMIAJIJEQI-WDCZJNDASA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.165 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.133 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.625	α = 90
b = 102.37	β = 90
c = 50.356	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-03 
Deposition Author(s): Vincent, F., Davies, G.J.

Revision History  

• Version 1.0: 2004-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description