3ZCT

Rabbit muscle glycogen phosphorylase b in complex with N-(2-naphthoyl) -N-beta-D-glucopyranosyl urea determined at 2.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ZCT/pdb

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


• Deposited: 2012-11-21 Released: 2013-12-11 
• Deposition Author(s): Chrysina, E.D., Nagy, V., Felfoldi, N., Konya, B., Telepo, K., Praly, J.P., Docsa, T., Gergely, P., Alexacou, K.M., Hayes, J.M., Konstantakaki, M., Kardakaris, R., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G., Somsak, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Synthesis, Kinetic, Computational and Crystallographic Evaluation of N-Acyl-N-Beta-D- Glucopyranosyl)Ureas, Nanomolar Glucose Analogue Inhibitors of Glycogen Phosphorylase, Potential Antidiabetic Agents

Chrysina, E.D., Nagy, V., Felfoldi, N., Konya, B., Telepo, K., Praly, J.P., Docsa, T., Gergely, P., Alexacou, K.M., Hayes, J.M., Konstantakaki, M., Kardakaris, R., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G., Somsak, L.

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: 98.77 kDa 
• Atom Count: 7,013 
• Modelled Residue Count: 810 
• Deposited Residue Count: 843 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN PHOSPHORYLASE, MUSCLE FORM	A	843	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
VMP	C [auth A], E [auth A]	N-[[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]carbamoyl]naphthalene-2-carboxamide C18 H20 N2 O7 CWTXJPICSREUOK-OWVAZHOYSA-N
IMP	D [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VMP	BindingDB:  3ZCT	Ki: 350 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.208 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.346	α = 90
b = 128.346	β = 90
c = 116.498	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Chrysina, E.D., Nagy, V., Felfoldi, N., Konya, B., Telepo, K., Praly, J.P., Docsa, T., Gergely, P., Alexacou, K.M., Hayes, J.M., Konstantakaki, M., Kardakaris, R., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G., Somsak, L.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description