MolNFT v1 · #31853 · protein
A/NWS/WHALE/MAINE/1/84 (H1N9) reassortant influenza virus neuraminidase
2B8H: “A/NWS/WHALE/MAINE/1/84 (H1N9) reassortant influenza virus neuraminidase”. X-ray diffraction, 5 ligands (MAN, NAG, BMA), 18 pockets (best druggability 0.66). MolNFT v1 #31853 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2B8H
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- P05803
- Ligands
- MAN, NAG, BMA, SO4, CL
- Pockets
- 18 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 388 | 4% helix, 45% strand | P05803 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 25 copies · chains D, A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, A, B, C
- SO4 · Sulfate ion · ion · 29 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.66 | 0.77 | 80 | empty |
| 2 | 253 | 0.61 | 0.81 | 42 | SO4 |
| 3 | 304 | 0.61 | 0.79 | 45 | SO4 |
| 4 | 259 | 0.60 | 0.80 | 40 | SO4 |
| 5 | 149 | 0.58 | 0.83 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1685 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1669 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1656 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1648 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 2B8H · A/NWS/whale/Maine/1/84 (H1N9) reassortant influenza virus 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 P05803
- Elsewhere: RCSB PDB 2B8H · PDBe 2B8H · UniProt P05803
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