2PRJ

Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosphorylase B

• PDB DOI: https://doi.org/10.2210/pdb2PRJ/pdb
• Entry: 2PRJ supersedes: 1PRJ

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


• Deposited: 1998-12-11 Released: 1998-12-16 
• Deposition Author(s): Oikonomakos, N.G., Kontou, M., Zographos, S.E., Watson, K.A., Johnson, L.N., Bichard, C.J.F., Fleet, G.W.J., Acharya, K.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

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: 98.11 kDa 
• Atom Count: 7,061 
• Modelled Residue Count: 830 
• 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
IMP	D [auth A]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NBG	B [auth A]	N-acetyl-beta-D-glucopyranosylamine C8 H15 N O6 IBONACLSSOLHFU-JAJWTYFOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NBG	Binding MOAD:  2PRJ	Ki: 3.20e+4 (nM) from 1 assay(s)
	BindingDB:  2PRJ	Ki: min: 3.16e+4, max: 3.20e+4 (nM) from 2 assay(s)
	PDBBind:  2PRJ	Ki: 3.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.237 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.5	α = 90
b = 128.5	β = 90
c = 116.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-12-16 
Deposition Author(s): Oikonomakos, N.G., Kontou, M., Zographos, S.E., Watson, K.A., Johnson, L.N., Bichard, C.J.F., Fleet, G.W.J., Acharya, K.R.
• This entry supersedes: 1PRJ

Revision History  

• Version 1.0: 1998-12-16
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Structure summary