Research workbench
Human sialidase 2 in complex with 2,3-difluorosialic acid (covalent intermediate)
Analyse Human sialidase 2 in complex with 2,3-difluorosialic acid (covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NCS
- Type
- protein
- Length
- 350 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase-2
- EC
- 3.2.1.18
- UniProt
- Q9Y3R4
- Ligands
- FSR, PO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase-2 (EC 3.2.1.18) | protein | 350 | 6% helix, 54% strand | Q9Y3R4 |
Ligands and binding sites
- FSR · (2S,3S,4R,5R,6R)-5-acetamido-2,3-bis(fluoranyl)-4-oxidanyl-6-[(1S,2S)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.64 | 0.79 | 29 | empty |
| 2 | 95 | 0.35 | 0.74 | 20 | FSR |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4NCS · Human sialidase 2 in complex with 2,3-difluorosialic acid (covalent intermediate) · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3R4 · AlphaFold monomer V2.0 prediction for sialidase-2 (Q9Y3R4) · a predicted model of the same protein · chain A 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 Q9Y3R4
- Elsewhere: RCSB PDB 4NCS · PDBe 4NCS · UniProt Q9Y3R4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.