3CUT

Crystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)oxamide

• PDB DOI: https://doi.org/10.2210/pdb3CUT/pdb

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


• Deposited: 2008-04-17 Released: 2009-04-21 
• Deposition Author(s): Kyritsi, C., Chrysina, E.D., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides

Czifrak, K., Kyritsi, C., Felfoldi, N., Dosca, T., Gergely, P., Chrysina, E.D., Siafaka-Kapadai, A., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 97.9 kDa 
• Atom Count: 6,826 
• Modelled Residue Count: 813 
• Deposited Residue Count: 842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
179	B [auth A]	N-[(naphthalen-2-ylamino)(oxo)acetyl]-beta-D-glucopyranosylamine C18 H20 N2 O7 WDRIXCWRSIXUDT-VPKNTQAGSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
179	BindingDB:  3CUT	Ki: 5.60e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.712	α = 90
b = 128.712	β = 90
c = 116.819	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Kyritsi, C., Chrysina, E.D., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection