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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

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

Organizational Affiliation

Roche Pharmaceuticals, Discovery Chemistry, F. Hoffmann-La Roche, Nutley, New Jersey 07110, USA. christine.lukacs@roche.com

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11217
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ADE Query on ADE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
SEP Query on 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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-03-21

Deposition Author(s):

Revision History (Full details and data files)

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