Research workbench
Structure of the human cytosolic sialidase NEU2 in complex with the inhibitor dana
Analyse Structure of the human cytosolic sialidase NEU2 in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VCU
- Type
- protein
- Length
- 743 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase 2
- EC
- 3.2.1.18
- UniProt
- Q9Y3R4
- Ligands
- DAN
- Pockets
- 9 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase 2 (EC 3.2.1.18) | protein | 370 | 8% helix, 48% strand | Q9Y3R4 |
| B | Sialidase 2 (EC 3.2.1.18) | protein | 373 | 6% helix, 51% strand | Q9Y3R4 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.65 | 0.86 | 28 | DAN |
| 2 | 171 | 0.63 | 0.85 | 30 | DAN |
| 3 | 331 | 0.63 | 0.79 | 27 | empty |
| 4 | 300 | 0.63 | 0.80 | 24 | empty |
| 5 | 298 | 0.51 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 333 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1VCU · Structure of the human cytosolic sialidase Neu2 in complex with the inhibitor DANA · 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 B against A, TM-score 1.00
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 1VCU · PDBe 1VCU · UniProt Q9Y3R4
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