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
View more details

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. [email protected]

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

Find similar proteins by:

(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

View Full Validation Report

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