MolNFT v1 · #118979 · protein
Open form of murine acid sphingomyelinase
5FIB · Sphingomyelin phosphodiesterase: “Open form of murine acid sphingomyelinase”. X-ray diffraction, 6 ligands (NAG, MAN, FUC), 7 pockets (best druggability 0.83). MolNFT v1 #118979 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5FIB
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingomyelin phosphodiesterase
- EC
- 3.1.4.12
- UniProt
- Q04519
- Ligands
- NAG, MAN, FUC, BMA, ZN, SO4
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 534 | 39% helix, 14% strand | Q04519 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.83 | 0.84 | 98 | empty |
| 2 | 225 | 0.47 | 0.73 | 45 | SO4 |
| 3 | 103 | 0.36 | 0.74 | 26 | empty |
| 4 | 80 | 0.36 | 0.76 | 26 | empty |
| 5 | 94 | 0.35 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 729 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 9 glycan (disulfide, N-glycosylation).
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 Q04519
- Elsewhere: RCSB PDB 5FIB · PDBe 5FIB · UniProt Q04519
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