MolNFT v1 · #121281 · protein
Catalytic domain of murine acid sphingomyelinase (asmase, asm, SMPD1)
5HQN · Sphingomyelin phosphodiesterase: “Catalytic domain of murine acid sphingomyelinase (asmase, asm, SMPD1)”. X-ray diffraction, 4 ligands (NAG, FUC, ZN), 5 pockets (best druggability 0.79). MolNFT v1 #121281 on GenesisL1: 3D structure…
- PDB
- 5HQN
- Type
- protein
- Length
- 884 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, FUC, ZN, PO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 442 | 33% helix, 17% strand | Q04519 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.79 | 0.82 | 68 | empty |
| 2 | 116 | 0.71 | 0.92 | 23 | empty |
| 3 | 239 | 0.51 | 0.76 | 35 | empty |
| 4 | 92 | 0.30 | 0.72 | 30 | PO4 |
| 5 | 54 | 0.26 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5HQN · Catalytic domain of murine Acid Sphingomyelinase (ASMase, ASM, SMPD1) · 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 0.99
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 5HQN · PDBe 5HQN · UniProt Q04519
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