MolNFT v1 · #189380 · protein
2.56 a structure of influenza hemagglutinin (ha) trimer
7VDF: “2.56 a structure of influenza hemagglutinin (ha) trimer”. Electron microscopy, 2 ligands (NAG, BMA), 15 pockets (best druggability 0.83). MolNFT v1 #189380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VDF
- Type
- protein
- Length
- 1,455 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q91MA7
- Ligands
- NAG, BMA
- Pockets
- 15 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Hemagglutinin | protein | 485 | 24% helix, 32% strand | Q91MA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.83 | 0.84 | 102 | empty |
| 2 | 543 | 0.72 | 0.81 | 49 | empty |
| 3 | 492 | 0.71 | 0.81 | 59 | empty |
| 4 | 434 | 0.68 | 0.80 | 45 | empty |
| 5 | 50 | 0.61 | 0.93 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2358 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2342 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2335 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7VDF · 2.56 A structure of influenza hemagglutinin (HA) trimer · 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 Q91MA7
- Elsewhere: RCSB PDB 7VDF · PDBe 7VDF · UniProt Q91MA7
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