MolNFT v1 · #123314 · protein
Crystal structure of human acid sphingomyelinase
5JG8 · Sphingomyelin phosphodiesterase: “Crystal structure of human acid sphingomyelinase”. X-ray diffraction, 3 ligands (NAG, MAN, ZN), 8 pockets (best druggability 0.61). MolNFT v1 #123314 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JG8
- Type
- protein
- Length
- 1,059 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingomyelin phosphodiesterase
- EC
- 3.1.4.12
- UniProt
- P17405
- Ligands
- NAG, MAN, ZN
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 529 | 37% helix, 16% strand | P17405 |
| B | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 530 | 37% helix, 15% strand | P17405 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.61 | 0.91 | 19 | empty |
| 2 | 186 | 0.61 | 0.83 | 32 | empty |
| 3 | 170 | 0.61 | 0.83 | 29 | empty |
| 4 | 193 | 0.56 | 0.79 | 36 | ACT |
| 5 | 237 | 0.51 | 0.75 | 35 | ACT |
Interfaces
1 interface between chains.
- A–B · 1825 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide, 12 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 P17405
- Elsewhere: RCSB PDB 5JG8 · PDBe 5JG8 · UniProt P17405
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