2ZB2

Human liver glycogen phosphorylase a complexed with glcose and 5-chloro-N-[4-(1,2-dihydroxyethyl)phenyl]-1H-indole-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb2ZB2/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-15 Released: 2008-09-02 
• Deposition Author(s): Katayama, N., Onda, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.307 
• R-Value Work: 0.261 
• R-Value Observed: 0.300 

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: 196.98 kDa 
• Atom Count: 13,413 
• Modelled Residue Count: 1,589 
• Deposited Residue Count: 1,698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, liver form	A, B	849	Homo sapiens	Mutation(s): 0  Gene Names: PYGL EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens) Explore P06737  Go to UniProtKB:  P06737
PHAROS:  P06737 GTEx:  ENSG00000100504

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A46	F [auth A], J [auth B]	5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide C17 H15 Cl N2 O3 SHCHFGSUYJUEBR-INIZCTEOSA-N
PLP	E [auth A], I [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MES	D [auth A], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GLC	C [auth A], G [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MPD	K [auth B], L [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A46	Binding MOAD:  2ZB2	IC50: 900 (nM) from 1 assay(s)
	BindingDB:  2ZB2	IC50: 900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.307 
• R-Value Work: 0.261 
• R-Value Observed: 0.300 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.819	α = 90
b = 123.819	β = 90
c = 123.538	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Katayama, N., Onda, K.

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary