MolNFT v1 · #121893 · protein
Asmase with zinc
5I8R · Sphingomyelin phosphodiesterase: “Asmase with zinc”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 12 pockets (best druggability 0.74). MolNFT v1 #121893 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5I8R
- Type
- protein
- Length
- 1,584 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingomyelin phosphodiesterase
- EC
- 3.1.4.12
- UniProt
- P17405
- Ligands
- NAG, BMA, MAN, ZN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 528 | 38% helix, 15% strand | P17405 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.74 | 0.78 | 96 | empty |
| 2 | 660 | 0.74 | 0.80 | 74 | empty |
| 3 | 140 | 0.60 | 0.84 | 31 | empty |
| 4 | 203 | 0.46 | 0.74 | 34 | empty |
| 5 | 111 | 0.38 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 672 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 656 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 13 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 5I8R · PDBe 5I8R · UniProt P17405
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