3BQP

Crystal Structure of Human Saposin D (orthorhombic)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the human ceramide activator protein saposin D.

Popovic, K.Prive, G.G.

(2008) Acta Crystallogr.,Sect.D 64: 589-594

  • DOI: 10.1107/S0907444908003120
  • Primary Citation of Related Structures:  3BQQ

  • PubMed Abstract: 
  • Saposin D is a sphingolipid activator protein required for the lysosomal breakdown of ceramide to a fatty acid and sphingosine by acid ceramidase. The crystal structure of saposin D has been determined in two different crystal forms, resulting in a t ...

    Saposin D is a sphingolipid activator protein required for the lysosomal breakdown of ceramide to a fatty acid and sphingosine by acid ceramidase. The crystal structure of saposin D has been determined in two different crystal forms, resulting in a total of six crystallographically independent views of this small 80-amino-acid protein. All of the structures are highly similar and reveal the monomeric form of the saposin fold previously seen in the crystal structures of saposins A and C. Saposin D is slightly more compact than the related saposins A and C owing to a slight repositioning of the 'stem' and 'hairpin' regions of the protein.


    Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proactivator polypeptide
A, B
80Homo sapiensGene Names: PSAP (GLBA, SAP1)
Find proteins for P07602 (Homo sapiens)
Go to Gene View: PSAP
Go to UniProtKB:  P07602
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.450α = 90.00
b = 61.450β = 90.00
c = 64.570γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
SHELXmodel building
SCALEPACKdata scaling
SHELXL-97refinement
SHELXphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance