1Z8D

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

Structural Biology Knowledgebase: 1Z8D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Z8D

Classification: TRANSFERASE

Total Structure Weight: 98197.42

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen phosphorylase, muscle form A 842 Homo sapiens EC#: 2.4.1.1 IUBMB
Mutation: S14X, K680X
Gene Name(s): PYGM Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AMP
Query on AMP

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADE
Query on ADE

A ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
A L-PEPTIDE LINKING C3 H8 N O6 P SER
LLP
Query on LLP
A L-PEPTIDE LINKING C14 H22 N3 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.192
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 92.37 α = 90.00
b = 144.00 β = 90.00
c = 59.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-03-30
  • 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

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4