MolNFT v1 · #118781 · protein
Murine SMPDL3A in complex with AMP
5FCB · Acid sphingomyelinase-like phosphodiesterase 3A: “Murine SMPDL3A in complex with AMP”. X-ray diffraction, 6 ligands (AMP, NAG, FUC), 3 pockets (best druggability 0.52). MolNFT v1 #118781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5FCB
- Type
- protein
- Length
- 426 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid sphingomyelinase-like phosphodiesterase 3A
- EC
- 3.1.4.-
- UniProt
- P70158
- Ligands
- AMP, NAG, FUC, MAN, BMA, ZN
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid sphingomyelinase-like phosphodiesterase 3A (EC 3.1.4.-) | protein | 426 | 36% helix, 17% strand | P70158 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 10 copies · 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 | 262 | 0.52 | 0.75 | 40 | AMP, GOL |
| 2 | 69 | 0.39 | 0.79 | 19 | empty |
| 3 | 92 | 0.37 | 0.76 | 24 | GOL |
Modifications
Observed in the structure: 4 glycan, 3 disulfide (N-glycosylation, disulfide).
Compared structures
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 P70158
- Elsewhere: RCSB PDB 5FCB · PDBe 5FCB · UniProt P70158
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