1PS3

Golgi alpha-mannosidase II in complex with kifunensine

Structural Biology Knowledgebase: 1PS3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 1PS3

Classification: HYDROLASE

Total Structure Weight: 120231.42

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-mannosidase II A 1045 Drosophila melanogaster EC#: 3.2.1.114 IUBMB
Gene Name(s): alpha-Man-II GmII CG18802
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KIF
Query on KIF

A KIFUNENSINE
C8 H12 N2 O6
OIURYJWYVIAOCW-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MRD
Query on MRD

A (4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
KIF N/A in BindingDB
Ki: 5200000 nM  BindingMOAD
Ki: 5200000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.200
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.09 α = 90.00
b = 109.80 β = 90.00
c = 138.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-20
  • Released Date: 2003-12-16
  • Deposition author(s): Shah, N., Kuntz, D.A., Rose, D.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update