MolNFT v1 · #36328 · protein
Crystal structure of the human sialidase NEU2 Q116E mutant in complex with dana inhibitor
2F29 · Sialidase 2: “Crystal structure of the human sialidase NEU2 Q116E mutant in complex with dana inhibitor”. X-ray diffraction, 1 ligand (DAN), 8 pockets (best druggability 0.71). MolNFT v1 #36328 on GenesisL1: 3D structure, binding…
- PDB
- 2F29
- Type
- protein
- Length
- 740 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
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sialidase 2 (EC 3.2.1.18) | protein | 370 | 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.71 | 0.87 | 39 | empty |
| 2 | 320 | 0.64 | 0.80 | 27 | empty |
| 3 | 308 | 0.63 | 0.80 | 29 | empty |
| 4 | 203 | 0.59 | 0.81 | 34 | DAN, EPE |
| 5 | 172 | 0.59 | 0.82 | 31 | DAN |
Interfaces
1 interface between chains.
- A–B · 1008 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2F29 · Crystal Structure of the Human Sialidase Neu2 Q116E Mutant in Complex with DANA Inhibitor · the same entry in another collection · chain B against B, 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 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 2F29 · PDBe 2F29 · UniProt Q9Y3R4
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