› 5ebb

X-ray diffraction
2.6Å resolution

Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+

Released:
DOI: 10.2210/pdb5ebb/pdb
PDB entry 5ebb coloured by chain, front view.
PDB entry 5ebb coloured by chain, side view.
PDB entry 5ebb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
Lim SM, Yeung K, Trésaugues L, Ling TH, Nordlund P
FEBS J 283 1107-23 (2016)
PMID: 26783088

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187667 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclic GMP-AMP phosphodiesterase SMPDL3A Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 410 amino acids
Theoretical weight: 46.61 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92484 (Residues: 34-443; Coverage: 95%)
Gene names: ASML3A, SMPDL3A
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 6 x ZN
Ligand NAG 9 x NAG
Ligand MLI 3 x MLI
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P3221
Unit cell:
a: 147.79Å b: 147.79Å c: 139.9Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.238 0.237 0.255
Expression system: Spodoptera frugiperda

Quick links

Citations

7 citation in other articles

Crystal structure of mammalian acid sphingomyelinase.
Gorelik et al. (2016)
6 more

2 mentions without citation

The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.
Lim et al. (2016)
1 more