› 5eud

X-ray diffraction
2.24Å resolution

S1P Lyase Bacterial Surrogate bound to N-(1-(4-(3-hydroxyprop-1-yn-1-yl)phenyl)-2-((4-methoxy-2,5-dimethylbenzyl)amino)ethyl)-5-methylisoxazole-3-carboxamide

Released:
DOI: 10.2210/pdb5eud/pdb
PDB entry 5eud coloured by chain, front view.
PDB entry 5eud coloured by chain, side view.
PDB entry 5eud coloured by chain, top view.
Source organism: Symbiobacterium thermophilum IAM 14863
Primary publication:
Creation of a S1P Lyase bacterial surrogate for structure-based drug design.
Argiriadi MA, Banach D, Radziejewska E, Marchie S, DiMauro J, Dinges J, Dominguez E, Hutchins C, Judge RA, Queeney K, Wallace G, Harris CM
Bioorg Med Chem Lett 26 2293-6 (2016)
PMID: 27013389

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179311 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Putative sphingosine-1-phosphate lyase Chains: A, B
Molecule details ›
Chains: A, B
Length: 514 amino acids
Theoretical weight: 55.74 KDa
Source organism: Symbiobacterium thermophilum IAM 14863
Expression system: Escherichia coli
UniProt:
  • Canonical: Q67PY4 (Residues: 2-507; Coverage: 100%)
Gene name: STH1274
Sequence domains: Pyridoxal-dependent decarboxylase conserved domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PO4 2 x PO4
Ligand 5S6 2 x 5S6
1 modified residue:
Ligand LLP 2 x LLP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 83.94Å b: 85.126Å c: 129.507Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.162 0.206
Expression system: Escherichia coli

Quick links

Citations

1 review citation

S1P Lyase Regulation of Thymic Egress and Oncogenic Inflammatory Signaling.
Kumar et al. (2017)
3 other articles

3 mentions without citation

Sphingolipid biosynthesis in man and microbes.
Harrison et al. (2018)
2 more