1L5Q

Human liver glycogen phosphorylase a complexed with caffeine, N-Acetyl-beta-D-glucopyranosylamine, and CP-403700

• PDB DOI: https://doi.org/10.2210/pdb1L5Q/pdb

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


• Deposited: 2002-03-07 Released: 2002-12-04 
• Deposition Author(s): Ekstrom, J.L., Pauly, T.A., Carty, M.D., Soeller, W.C., Culp, J., Danley, D.E., Hoover, D.J., Treadway, J.L., Gibbs, E.M., Fletterick, R.J., Day, Y.S.N., Myszka, D.G., Rath, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 197.12 kDa 
• Atom Count: 13,620 
• Modelled Residue Count: 1,581 
• Deposited Residue Count: 1,694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, liver form	A, B	847	Homo sapiens	Mutation(s): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
700	E [auth A], J [auth B]	[5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID C22 H20 Cl N3 O4 RONLONYAIBUEKT-IBGZPJMESA-N
PLP	D [auth A], I [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
NBG	C [auth A], H [auth B]	N-acetyl-beta-D-glucopyranosylamine C8 H15 N O6 IBONACLSSOLHFU-JAJWTYFOSA-N
CFF	F [auth A], G [auth A], K [auth B], L [auth B]	CAFFEINE C8 H10 N4 O2 RYYVLZVUVIJVGH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
700	Binding MOAD:  1L5Q	IC50: 145 (nM) from 1 assay(s)
	BindingDB:  1L5Q	IC50: 45 (nM) from 1 assay(s)
CFF	PDBBind:  1L5Q	Kd: 1.08e+5 (nM) from 1 assay(s)
	Binding MOAD:  1L5Q	Kd: 1.08e+5 (nM) from 1 assay(s)
	BindingDB:  1L5Q	IC50: 6.48e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.240 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.713	α = 90
b = 124.713	β = 90
c = 124.45	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-04 
Deposition Author(s): Ekstrom, J.L., Pauly, T.A., Carty, M.D., Soeller, W.C., Culp, J., Danley, D.E., Hoover, D.J., Treadway, J.L., Gibbs, E.M., Fletterick, R.J., Day, Y.S.N., Myszka, D.G., Rath, V.L.

Revision History  

• Version 1.0: 2002-12-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2012-05-02
  Changes: Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary