3BD8

Glucogen Phosphorylase complex with 1(-D-glucopyranosyl) cytosine

• PDB DOI: https://doi.org/10.2210/pdb3BD8/pdb

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


• Deposited: 2007-11-14 Released: 2008-11-18 
• Deposition Author(s): Sovantzis, D.A., Hadjiloi, T., Hayes, J.M., Zographos, S.E., Chrysina, E.D., Oikonomakos, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.211 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b

Cisma, C., Sovantzis, D.A., Hadjiloi, T., Stathis, D., Gimisis, T., Hayes, J.M., Zographos, S.E., Leonidas, D.D., Chrysina, E.D., Oikonomakos, N.G.

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: 97.81 kDa 
• Atom Count: 6,970 
• Modelled Residue Count: 810 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C3B	C [auth A]	4-amino-1-beta-D-glucopyranosylpyrimidin-2(1H)-one C10 H15 N3 O6 YYUQXKHCNLFJNF-DDIGBBAMSA-N
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C3B	BindingDB:  3BD8	Ki: 7700 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.211 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.591	α = 90
b = 128.591	β = 90
c = 116.254	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Sovantzis, D.A., Hadjiloi, T., Hayes, J.M., Zographos, S.E., Chrysina, E.D., Oikonomakos, N.G.

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary