Research workbench
Crystal structure of the human sialidase NEU2 in complex with 2',3'- dihydroxypropyl ether mimetic inhibitor
Analyse Crystal structure of the human sialidase NEU2 in complex with 2',3'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F13
- Type
- protein
- Length
- 351 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
- DYM, PO4
- Pockets
- 2 · best druggability 0.62
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 | 351 | 6% helix, 54% strand | Q9Y3R4 |
Ligands and binding sites
- DYM · (2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 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 | 317 | 0.62 | 0.79 | 27 | empty |
| 2 | 97 | 0.36 | 0.74 | 19 | DYM |
Compared structures
- 2F13 · Crystal Structure of the Human Sialidase Neu2 in Complex with 2',3'- dihydroxypropyl… · 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 2F13 · PDBe 2F13 · UniProt Q9Y3R4
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