MolNFT v1 · #118780 · protein
Murine SMPDL3A in presence of excess zinc
5FCA · Acid sphingomyelinase-like phosphodiesterase 3A: “Murine SMPDL3A in presence of excess zinc”. X-ray diffraction, 5 ligands (NAG, FUC, MAN), 4 pockets (best druggability 0.69). MolNFT v1 #118780 on GenesisL1: 3D structure, binding…
- PDB
- 5FCA
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- 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
- NAG, FUC, MAN, BMA, ZN
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acid sphingomyelinase-like phosphodiesterase 3A (EC 3.1.4.-) | protein | 426 | 35% helix, 17% strand | P70158 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 8 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.69 | 0.74 | 119 | ZN, GOL |
| 2 | 110 | 0.41 | 0.77 | 27 | empty |
| 3 | 74 | 0.40 | 0.79 | 17 | empty |
| 4 | 63 | 0.36 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 687 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 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 5FCA · PDBe 5FCA · UniProt P70158
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