Research workbench
Open form of murine acid sphingomyelinase in presence of lipid
Analyse Open form of murine acid sphingomyelinase in presence of lipid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FIC
- Type
- protein
- Length
- 2,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingomyelin phosphodiesterase
- EC
- 3.1.4.12
- UniProt
- Q04519
- Ligands
- 6E0, NAG, BMA, FUC, ZN, PO4, CL
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 527 | 39% helix, 14% strand | Q04519 |
Ligands and binding sites
- 6E0 · octadecylphosphonic acid · ligand · 2 copies · chains A, C, B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 7 copies · chains A, B, D, C
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.80 | 0.84 | 77 | CL |
| 2 | 104 | 0.66 | 0.90 | 21 | empty |
| 3 | 120 | 0.65 | 0.88 | 24 | empty |
| 4 | 176 | 0.62 | 0.83 | 27 | empty |
| 5 | 546 | 0.62 | 0.74 | 45 | PO4, 6E0 |
Interfaces
3 interfaces between chains.
- A–B · 732 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 511 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 5FIC · Open form of murine Acid Sphingomyelinase in presence of lipid · the same entry in another collection · chain D against D, TM-score 1.00
- Q04519 · AlphaFold monomer V2.0 prediction for sphingomyelin phosphodiesterase (Q04519) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q04519
- Elsewhere: RCSB PDB 5FIC · PDBe 5FIC · UniProt Q04519
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