› 5kar

X-ray diffraction
1.14Å resolution

Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B)

Released:
DOI: 10.2210/pdb5kar/pdb
PDB entry 5kar coloured by chain, front view.
PDB entry 5kar coloured by chain, side view.
PDB entry 5kar coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.
Gorelik A, Heinz LX, Illes K, Superti-Furga G, Nagar B
J Biol Chem 291 24054-24064 (2016)
PMID: 27687724

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-157661 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (4 distinct):
Acid sphingomyelinase-like phosphodiesterase 3b Chain: A
Molecule details ›
Chain: A
Length: 427 amino acids
Theoretical weight: 48.81 KDa
Source organism: Mus musculus
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P58242 (Residues: 19-435; Coverage: 95%)
Gene names: Asml3b, Smpdl3b
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
3 bound ligands:
Ligand ZN 2 x ZN
Ligand NO3 2 x NO3
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P2
Unit cell:
a: 50.892Å b: 47.031Å c: 93.861Å
α: 90° β: 98.07° γ: 90°
R-values:
R R work R free
0.136 0.135 0.152
Expression system: Spodoptera frugiperda

Quick links

Citations

2 review citations

Podocyte Sphingolipid Signaling in Nephrotic Syndrome.
Li et al. (2021)
1 more

1 mention without citation

Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity.
Gorelik et al. (2016)