6GPB

REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 6GPB

Classification: GLYCOGEN PHOSPHORYLASE

Total Structure Weight: 99407.73

Macromolecule Entities
Molecule Chains Length Organism Details
GLYCOGEN PHOSPHORYLASE B A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Mutation: L380I
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H2P
Query on H2P

A HEPTULOSE-2-PHOSPHATE
C7 H15 O9 P
QZBAZODTRUGOQS-XUUWZHRGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
H2P N/A in BindingDB
N/A in BindingMoad
Ki: 14000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Observed:
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.50 α = 90.00
b = 128.50 β = 90.00
c = 116.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1990-06-04
  • Released Date: 1992-10-15
  • Deposition author(s): Acharya, K.R., Johnson, L.N.

Revision History

  • Version 1_0: 1992-10-15

    Type: Initial release

  • Version 1_1: 2008-03-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Derived calculations, Version format compliance