1Z8D

Crystal Structure of Human Muscle Glycogen Phosphorylase a with AMP and Glucose

• PDB DOI: https://doi.org/10.2210/pdb1Z8D/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2005-03-30 Released: 2006-03-21 
• Deposition Author(s): Lukacs, C.M., Oikonomakos, N.G., Crowther, R.L., Hong, L.N., Kammlott, R.U., Levin, W., Li, S., Liu, C.M., Lucas-McGady, D., Pietranico, S., Reik, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.192 

Starting Model: experimental

Literature

The crystal structure of human muscle glycogen phosphorylase a with bound glucose and AMP: An intermediate conformation with T-state and R-state features.

Lukacs, C.M., Oikonomakos, N.G., Crowther, R.L., Hong, L.N., Kammlott, R.U., Levin, W., Li, S., Liu, C.M., Lucas-McGady, D., Pietranico, S., Reik, L.

(2006) Proteins 63: 1123-1126

• PubMed: 16523484 
• DOI: https://doi.org/10.1002/prot.20939
• Primary Citation of Related Structures:  
  1Z8D

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Organizational Affiliation: 

Roche Pharmaceuticals, Discovery Chemistry, F. Hoffmann-La Roche, Nutley, New Jersey 07110, USA. [e-mail]

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: 98.19 kDa 
• Atom Count: 7,121 
• Modelled Residue Count: 821 
• 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	Homo sapiens	Mutation(s): 2  Gene Names: PYGM EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11217 (Homo sapiens) Explore P11217  Go to UniProtKB:  P11217
PHAROS:  P11217 GTEx:  ENSG00000068976

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
ADE	D [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.192 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.37	α = 90
b = 144	β = 90
c = 59.44	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Lukacs, C.M., Oikonomakos, N.G., Crowther, R.L., Hong, L.N., Kammlott, R.U., Levin, W., Li, S., Liu, C.M., Lucas-McGady, D., Pietranico, S., Reik, L.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection