› 5ebe

X-ray diffraction
3Å resolution

Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5' CMP

Released:
DOI: 10.2210/pdb5ebe/pdb
PDB entry 5ebe coloured by chain, front view.
PDB entry 5ebe coloured by chain, side view.
PDB entry 5ebe 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:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
Cyclic GMP-AMP phosphodiesterase SMPDL3A Chain: A
Molecule details ›
Chain: A
Length: 418 amino acids
Theoretical weight: 47.6 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92484 (Residues: 33-450; Coverage: 97%)
Gene names: ASML3A, SMPDL3A
Sequence domains:
Cyclic GMP-AMP phosphodiesterase SMPDL3A Chains: B, C
Molecule details ›
Chains: B, C
Length: 415 amino acids
Theoretical weight: 47.19 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92484 (Residues: 33-447; Coverage: 96%)
Gene names: ASML3A, SMPDL3A
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
7 bound ligands:
Ligand NAG 11 x NAG
Ligand ZN 6 x ZN
Ligand C5P 2 x C5P
Ligand GOL 2 x GOL
Ligand MLI 1 x MLI
Ligand RP5 1 x RP5
Ligand SCN 2 x SCN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P3221
Unit cell:
a: 147.654Å b: 147.654Å c: 142.298Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.254 0.251 0.295
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