› 5fc1

X-ray diffraction
1.39Å resolution

Murine SMPDL3A in complex with sulfate

Released:
DOI: 10.2210/pdb5fc1/pdb
PDB entry 5fc1 coloured by chain, front view.
PDB entry 5fc1 coloured by chain, side view.
PDB entry 5fc1 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural Basis for Nucleotide Hydrolysis by the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3A.
Gorelik A, Illes K, Superti-Furga G, Nagar B
J Biol Chem 291 6376-85 (2016)
PMID: 26792860

Function and Biology Details

Reaction catalysed: 
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159706 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Cyclic GMP-AMP phosphodiesterase SMPDL3A Chain: A
Molecule details ›
Chain: A
Length: 433 amino acids
Theoretical weight: 49 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P70158 (Residues: 23-445; Coverage: 100%)
Gene names: Asml3a, Smpdl3a
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand ZN 2 x ZN
Ligand NAG 1 x NAG
Ligand SO4 1 x SO4
Ligand GOL 12 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2221
Unit cell:
a: 123.65Å b: 131.87Å c: 80.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.13 0.161
Expression system: Spodoptera frugiperda

Quick links

Citations

6 citation in other articles

Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.
Xiong et al. (2016)
5 more

2 mentions without citation

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