9I63 | pdb_00009i63

Synthetic Human Saposin D glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb9I63/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2025-01-29 Released: 2025-04-09 
• Deposition Author(s): Weyand, M., Unverzagt, C.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.201 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.176 (DCC) 

Starting Model: experimental

Literature

Synthetic Glycoforms Reveal Carbohydrate-Dependent Bioactivity of Human Saposin D.

Graf, C.G.F., Schulz, C., Schmalzlein, M., Heinlein, C., Monnich, M., Perkams, L., Puttner, M., Boos, I., Hessefort, M., Lombana Sanchez, J.N., Weyand, M., Steegborn, C., Breiden, B., Ross, K., Schwarzmann, G., Sandhoff, K., Unverzagt, C.

(2017) Angew Chem Int Ed Engl 56: 5252-5257

• PubMed: 28378443 
• DOI: https://doi.org/10.1002/anie.201701362
• Primary Citation of Related Structures:  
  9I63


• PubMed Abstract: 
  

  The main glycoforms of the hydrophobic lysosomal glycoprotein saposin D (SapD) were synthesized by native chemical ligation. An approach for the challenging solid-phase synthesis of the fragments was developed. Three SapD glycoforms were obtained following a general and robust refolding and purification protocol. A crystal structure of one glycoform confirmed its native structure and disulfide pattern. Functional assays revealed that the lipid-binding properties of three SapD glycoforms are highly affected by the single sugar moiety of SapD showing a dependency of the size and the type of N-glycan.

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Organizational Affiliation: 
• Bioorg. Chemie, Gebäude NWI, Universität Bayreuth, 95440, Bayreuth, Germany.
Department of Biochemistry, Universität Bayreuth, Germany.
LIMES Institute, Universität Bonn, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.33 kDa 
• Atom Count: 1,501 
• Modeled Residue Count: 156 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prosaposin	A, B	82	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P07602 (Homo sapiens) Explore P07602  Go to UniProtKB:  P07602
PHAROS:  P07602 GTEx:  ENSG00000197746

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	A, B	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.201 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.176 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.44	α = 90
b = 65.68	β = 114.498
c = 42.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Weyand, M., Unverzagt, C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	UN63/5-1

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release