MolNFT v1 · #146155 · protein
Structure of influenza neuraminidase from strain A/BREVIGMISSION/1/1918(H1N1) expressed in hek-293E cells
6D96: “Structure of influenza neuraminidase from strain A/BREVIGMISSION/1/1918(H1N1) expressed in hek-293E cells”. X-ray diffraction, 3 ligands (NAG, FUC, CA), 20 pockets (best druggability 0.66). MolNFT v1 #146155 on GenesisL1: 3D…
- PDB
- 6D96
- Type
- protein
- Length
- 3,088 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q9IGQ6
- Ligands
- NAG, FUC, CA
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Neuraminidase (EC 3.2.1.18) | protein | 386 | 3% helix, 46% strand | Q9IGQ6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains B, C, D, E, F, G, H, A
- FUC · alpha-L-fucopyranose · sugar · 7 copies · chains B, C, D, E, F, G, H
- CA · Calcium ion · metal · 18 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 6 copies · chains A, C, D, E, 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 | 358 | 0.66 | 0.81 | 51 | empty |
| 2 | 372 | 0.66 | 0.80 | 54 | empty |
| 3 | 344 | 0.65 | 0.80 | 50 | empty |
| 4 | 368 | 0.65 | 0.80 | 49 | empty |
| 5 | 380 | 0.64 | 0.79 | 53 | empty |
Interfaces
13 interfaces between chains.
- B–D · 1594 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1590 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1586 Ų buried · 20 hydrogen bonds · protein-protein
- F–G · 1576 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1569 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 6D96 · Structure of influenza neuraminidase from strain A/BrevigMission/1/1918(H1N1) expressed… · 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 Q9IGQ6
- Elsewhere: RCSB PDB 6D96 · PDBe 6D96 · UniProt Q9IGQ6
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