Research workbench
N1 neuraminidase
Analyse N1 neuraminidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HTY
- Type
- protein
- Length
- 3,080 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- Q6DPL2
- Ligands
- NDG, NAG, CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Neuraminidase | protein | 385 | 3% helix, 44% strand | Q6DPL2 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 7 copies · chains A, B, C, D, F, G, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- CA · Calcium ion · metal · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.68 | 0.81 | 51 | empty |
| 2 | 412 | 0.68 | 0.81 | 56 | empty |
| 3 | 409 | 0.68 | 0.81 | 60 | empty |
| 4 | 430 | 0.68 | 0.80 | 54 | empty |
| 5 | 378 | 0.68 | 0.81 | 50 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1635 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1635 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 1632 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1630 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1621 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 disulfide (disulfide).
Compared structures
- 2HTY · N1 neuraminidase · 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 2HTY · PDBe 2HTY · UniProt Q6DPL2
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