3BQP

Crystal Structure of Human Saposin D (orthorhombic)

• PDB DOI:  https://doi.org/10.2210/pdb3BQP/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-20 Released: 2008-02-05 
• Deposition Author(s): Prive, G.G., Popovic, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.234 
• R-Value Observed: 0.176 

Literature

Structures of the human ceramide activator protein saposin D.

Popovic, K., Prive, G.G.

(2008) Acta Crystallogr D Biol Crystallogr 64: 589-594

• PubMed: 18453694 
• DOI: https://doi.org/10.1107/S0907444908003120
• Primary Citation of Related Structures:  
  3BQP, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.93 kDa 
• Atom Count: 1,472 
• Modelled Residue Count: 160 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proactivator polypeptide	A, B	80	Homo sapiens	Mutation(s): 0  Gene Names: PSAP, GLBA, SAP1
UniProt & NIH Common Fund Data Resources
Find proteins for P07602 (Homo sapiens) Explore P07602  Go to UniProtKB:  P07602
PHAROS:  P07602

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.234 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.45	α = 90
b = 61.45	β = 90
c = 64.57	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Prive, G.G., Popovic, K.

Revision History  

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