2QNB

Glycogen Phosphorylase b in complex with N-benzoyl-N'-beta-D-glucopyranosyl urea

• PDB DOI: https://doi.org/10.2210/pdb2QNB/pdb

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


• Deposited: 2007-07-18 Released: 2008-07-22 
• Deposition Author(s): Chrysina, E.D., Tiraidis, C., Alexacou, K.-M., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation

Nagy, V., Felf ldi, N., Praly, J.-P., Docsa, T., Gergerly, P., Chrysina, E.D., Tiraidis, C., Kosmopoulou, M.N., Alexacou, K.-M., Konstantakaki, M.

To be published.

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 (software)

Macromolecule Content

• Total Structure Weight: 98.17 kDa 
• Atom Count: 7,004 
• Modelled Residue Count: 811 
• 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
BZD	B [auth A], C [auth A]	N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine C14 H18 N2 O7 JSBCZGSPFATCOV-BZNQNGANSA-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
BZD	PDBBind:  2QNB	Ki: 4600 (nM) from 1 assay(s)
	BindingDB:  2QNB	Ki: 4600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.653	α = 90
b = 128.653	β = 90
c = 116.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Chrysina, E.D., Tiraidis, C., Alexacou, K.-M., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-11-15
  Changes: Data collection