Research workbench
N1 neuraminidase N294S + oseltamivir
Analyse N1 neuraminidase N294S + oseltamivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CL2
- Type
- protein
- Length
- 3,080 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q6DPL2
- Ligands
- G39
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Neuraminidase (EC 3.2.1.18) | protein | 385 | 3% helix, 43% strand | Q6DPL2 |
Ligands and binding sites
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.65 | 0.82 | 44 | G39 |
| 2 | 290 | 0.65 | 0.81 | 44 | G39 |
| 3 | 273 | 0.65 | 0.82 | 38 | G39 |
| 4 | 287 | 0.64 | 0.81 | 41 | G39 |
| 5 | 287 | 0.64 | 0.81 | 41 | G39 |
Interfaces
13 interfaces between chains.
- F–G · 1627 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 1622 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1602 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1597 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 1594 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide (disulfide).
Compared structures
- 3CL2 · N1 Neuraminidase N294S + Oseltamivir · the same entry in another collection · 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 Q6DPL2
- Elsewhere: RCSB PDB 3CL2 · PDBe 3CL2 · UniProt Q6DPL2
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