2QRP

Glycogen Phosphorylase b in complex with (1R)-3'-(2-naphthyl)-spiro[1,5-anhydro-D-glucitol-1,5'-isoxazoline]

Structural Biology Knowledgebase: 2QRP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 2QRP

Classification: TRANSFERASE

Total Structure Weight: 99041.42

Macromolecule Entities
Molecule Chains Length Organism Details
Glycogen phosphorylase, muscle form A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
S06
Query on S06

A (3S,5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3- (2-naphthyl)-1,6-dioxa-2-azaspiro[4.5]decane- 8,9,10-triol
5'-isoxazoline],,5-anhydro-D- glucitol-1 (Synonym)
C18 H21 N O6
ZCJBDRSKHARECB-PYTCMNEWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
S06 N/A in BindingDB
Ki: 630 nM  BindingMOAD
Ki: 630 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
LLP
Query on LLP
A L-PEPTIDE LINKING C14 H22 N3 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.194
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 126.02 α = 90.00
b = 126.02 β = 90.00
c = 114.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-28
  • Released Date: 2008-07-29
  • Deposition author(s): Gizilis, G., Alexacou, K.M., Chrysina, E.D., Zographos, S.E., Leonidas, D.D., Oikonomakos, N.G.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4