8AYF

Crystal structure of human Sphingosine-1-phosphate lyase 1

• PDB DOI:  https://doi.org/10.2210/pdb8AYF/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-09-02 Released: 2023-09-13 
• Deposition Author(s): Giardina, G., Catalano, F., Pampalone, G., Cellini, B.
• Funding Organization(s): Other government, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.214 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

Crystal structure of human Sphingosine-1-phosphate lyase 1

Giardina, G., Catalano, F., Pampalone, G., Cellini, B.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 110.3 kDa 
• Atom Count: 7,239 
• Modelled Residue Count: 891 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine-1-phosphate lyase 1	A, B	494	Homo sapiens	Mutation(s): 0  Gene Names: SGPL1, KIAA1252 EC: 4.1.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O95470 (Homo sapiens) Explore O95470  Go to UniProtKB:  O95470
PHAROS:  O95470

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.214 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.16	α = 90
b = 127.41	β = 104.85
c = 66.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Giardina, G., Catalano, F., Pampalone, G., Cellini, B.

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Funding Organization	Location	Grant Number
Other government	Italy	RP11916B407928AA
Other government	Italy	RM12117A5BDD4AEC
Other private	Italy	FFC#16/2020

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release