MolNFT v1 · #124290 · protein
Murine acid sphingomyelinase-like phosphodiesterase 3B (SMPDL3B)
5KAR: “Murine acid sphingomyelinase-like phosphodiesterase 3B (SMPDL3B)”. X-ray diffraction, 6 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.58). MolNFT v1 #124290 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KAR
- Type
- protein
- Length
- 412 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid sphingomyelinase-like phosphodiesterase 3B
- EC
- 3.1.4.-
- UniProt
- P58242
- Ligands
- NAG, MAN, BMA, FUC, ZN, NO3
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid sphingomyelinase-like phosphodiesterase 3B (EC 3.1.4.-) | protein | 412 | 38% helix, 18% strand | P58242 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- NO3 · Nitrate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.58 | 0.83 | 29 | GOL |
| 2 | 52 | 0.34 | 0.79 | 18 | empty |
| 3 | 66 | 0.33 | 0.76 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5KAR · Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B) · the same entry in another collection · chain A against A, TM-score 1.00
- P58242 · AlphaFold monomer V2.0 prediction for acid sphingomyelinase-like phosphodiesterase 3B… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P58242
- Elsewhere: RCSB PDB 5KAR · PDBe 5KAR · UniProt P58242
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