Research workbench
Closed form of murine acid sphingomyelinase in complex with bisphosphonate inhibitor abpa
Analyse Closed form of murine acid sphingomyelinase in complex with bisphosphonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FI9
- Type
- protein
- Length
- 1,052 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
- NT8, NAG, FUC, BMA, MAN, ZN
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 523 | 38% helix, 15% strand | Q04519 |
| B | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 529 | 37% helix, 15% strand | Q04519 |
Ligands and binding sites
- NT8 · (1-azanyl-1-phosphono-decyl)phosphonic acid · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- ZN · Zinc ion · metal · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.79 | 0.80 | 107 | empty |
| 2 | 924 | 0.74 | 0.77 | 71 | NT8 |
| 3 | 546 | 0.64 | 0.76 | 52 | empty |
| 4 | 182 | 0.61 | 0.83 | 30 | empty |
| 5 | 138 | 0.58 | 0.83 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5FI9 · Closed form of murine Acid Sphingomyelinase in complex with bisphosphonate inhibitor AbPA · the same entry in another collection · chain A against A, TM-score 1.00
- Q04519 · AlphaFold monomer V2.0 prediction for sphingomyelin phosphodiesterase (Q04519) · a predicted model of the same protein · chain B against A, TM-score 0.86
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 5FI9 · PDBe 5FI9 · UniProt Q04519
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