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Crystal structure of the human neutral sphingomyelinase 2 (NSMASE2) catalytic domain with insertion deleted and calcium bound
Analyse Crystal structure of the human neutral sphingomyelinase 2 (NSMASE2) catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UVG
- Type
- protein
- Length
- 348 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingomyelin phosphodiesterase 3,SPHINGOMYELIN phosphodiesterase 3
- EC
- 3.1.4.12
- UniProt
- Q9NY59
- Ligands
- CA
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingomyelin phosphodiesterase 3,SPHINGOMYELIN phosphodiesterase 3 (EC 3.1.4.12) | protein | 348 | 24% helix, 32% strand | Q9NY59 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.47 | 0.75 | 26 | empty |
| 2 | 62 | 0.35 | 0.78 | 18 | empty |
| 3 | 52 | 0.27 | 0.74 | 12 | empty |
| 4 | 52 | 0.27 | 0.74 | 15 | empty |
| 5 | 50 | 0.25 | 0.74 | 14 | empty |
Compared structures
- 5UVG · Crystal structure of the human neutral sphingomyelinase 2 (nSMase2) catalytic domain with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NY59 · AlphaFold monomer V2.0 prediction for sphingomyelin phosphodiesterase 3 (Q9NY59) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9NY59
- Elsewhere: RCSB PDB 5UVG · PDBe 5UVG · UniProt Q9NY59
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