PDBsum entry 3bqq

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Lipid binding protein PDB id
Protein chains
79 a.a. *
Waters ×314
* Residue conservation analysis
PDB id:
Name: Lipid binding protein
Title: Crystal structure of human saposin d (triclinic)
Structure: Proactivator polypeptide. Chain: c, a, b, d. Fragment: saposin d, residues 405-484. Synonym: ceramide activator protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: psap. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.00Å     R-factor:   0.198     R-free:   0.242
Authors: G.G.Prive,K.Popovic
Key ref:
K.Popovic and G.G.Privé (2008). Structures of the human ceramide activator protein saposin D. Acta Crystallogr D Biol Crystallogr, 64, 589-594. PubMed id: 18453694 DOI: 10.1107/S0907444908003120
20-Dec-07     Release date:   05-Feb-08    
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Protein chains
Pfam   ArchSchema ?
P07602  (SAP_HUMAN) -  Prosaposin
524 a.a.
79 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     lysosome   1 term 
  Biological process     lipid metabolic process   2 terms 


DOI no: 10.1107/S0907444908003120 Acta Crystallogr D Biol Crystallogr 64:589-594 (2008)
PubMed id: 18453694  
Structures of the human ceramide activator protein saposin D.
K.Popovic, G.G.Privé.
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.
  Selected figure(s)  
Figure 1.
Figure 1 Structure of saposin D. (a) Ribbon representation of saposin D with helices 1, 2, 3 and 4 coloured blue, green, yellow and red, respectively. Disulfide bonds are indicated by black lines. (b) Superposition of the two molecules from the orthorhombic form (red and orange) and the four molecules from the triclinic form (yellow, green, blue and purple).
Figure 2.
Figure 2 Putative dimer of saposin D. (a) Ribbon representation of the association between chains A and B in the triclinic crystal form. Similar dimers are observed between chains C and D in the triclinic form and between chains A and B in the orthorhombic form. The conserved glycosylation site at residue Asn22 is indicated. (b) Close-up view of the interchain contact surface. Residues Pro42, Lys45, Gln46 and Gln49 are indicated. The dotted lines represent interchain hydrogen bonds between residues Gln46 and Gln49.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2008, 64, 589-594) copyright 2008.  
  Figures were selected by the author.