› 8h21

X-ray diffraction
1.54Å resolution

Serine Palmitoyltransferase from Sphingobacterium multivorum complexed with L-alanine

Released:
DOI: 10.2210/pdb8h21/pdb
Model geometry
Fit model/data
PDB entry 8h21 coloured by chain, front view.
PDB entry 8h21 coloured by chain, side view.
PDB entry 8h21 coloured by chain, top view.
Source organism: Sphingobacterium multivorum
Primary publication:
Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
Ikushiro H, Murakami T, Takahashi A, Katayama A, Sawai T, Goto H, Koolath S, Murai Y, Monde K, Miyahara I, Kamiya N, Yano T
OpenAccess logo J Biol Chem 299 104684 (2023)
PMID: 37030501

Function and Biology Details

Reaction catalysed: 
Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108244 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine palmitoyltransferase Chain: A
Molecule details ›
Chain: A
Length: 399 amino acids
Theoretical weight: 43.82 KDa
Source organism: Sphingobacterium multivorum
Expression system: Escherichia coli
UniProt:
  • Canonical: A7BFV6 (Residues: 1-399; Coverage: 100%)
Gene names: I6J33_20140, NCTC11343_02561, SPHINGO8BC_150128, spt
Sequence domains: Aminotransferase class I and II

Ligands and Environments

2 bound ligands:
Ligand EDO 6 x EDO
Ligand PDA 1 x PDA
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: RIGAKU FR-X
Spacegroup: P41212
Unit cell:
a: 61.234Å b: 61.234Å c: 208.182Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.172 0.216
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Structural insights into the substrate recognition of serine palmitoyltransferase from Sphingobacterium multivorum.
Ikushiro et al. (2023)