6SLR | pdb_00006slr

Structure of saposin B in complex with atovaquone

• PDB DOI: https://doi.org/10.2210/pdb6SLR/pdb

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


• Deposited: 2019-08-20 Released: 2020-09-09 
• Deposition Author(s): Zubieta, C., Milliken, B., Doyle, R.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.278 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Structure of saposin B in complex with atovaquone

Zubieta, C., Milliken, B., Doyle, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.91 kDa 
• Atom Count: 1,997 
• Modeled Residue Count: 240 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prosaposin	A, B, C	81	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 GTEx:  ENSG00000197746

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AOQ (Subject of Investigation/LOI)	F [auth B], G [auth C]	2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione C22 H19 Cl O3 KUCQYCKVKVOKAY-CTYIDZIISA-N
GOL	D [auth B], E [auth B], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.278 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.707	α = 90
b = 75.707	β = 90
c = 95.475	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Zubieta, C., Milliken, B., Doyle, R.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ATIP-Avenir

Revision History  

• Version 1.0: 2020-09-09
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary