1AXR | pdb_00001axr

COOPERATIVITY BETWEEN HYDROGEN-BONDING AND CHARGE-DIPOLE INTERACTIONS IN THE INHIBITION OF BETA-GLYCOSIDASES BY AZOLOPYRIDINES: EVIDENCE FROM A STUDY WITH GLYCOGEN PHOSPHORYLASE B

• PDB DOI: https://doi.org/10.2210/pdb1AXR/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 1997-10-20 Released: 1998-01-28 
• Deposition Author(s): Oikonomakos, N.G., Heightman, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.276 (Depositor) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Cooperative interactions of the catalytic nucleophile and the catalytic acid in the inhibition of beta-glycosidases. Calculations and their validation by comparative kinetic and structural studies of the inhibition of glycogen phosphorylase b.

Heightman, T.D., Vasella, A., Tsitsanou, K.E., Zographos, S.E., Skamnaki, V.T., Oikonomakos, N.G.

(1998) Helvetica Chim Acta 81: 853-864

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 97.93 kDa 
• Atom Count: 7,281 
• Modeled Residue Count: 829 
• Deposited Residue Count: 842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN PHOSPHORYLASE	A	842	Oryctolagus cuniculus	Mutation(s): 0  EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
HTP	E [auth A]	4,5,6-TRIHYDROXY-7-HYDROXYMETHYL-4,5,6,7-TETRAHYDRO-1H-[1,2,3]TRIAZOLO[1,5-A]PYRIDIN-8-YLIUM C7 H12 N3 O4 QTNWFPNNMUCBLD-XZBKPIIZSA-O
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.276 (Depositor) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.72	α = 90
b = 126.72	β = 90
c = 115.59	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Oikonomakos, N.G., Heightman, T.D.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other