MolNFT v1 · #158384 · protein
Crystal structure of the ivr-165 (H3N2) influenza virus hemagglutinin apo form
6NS9 · Hemagglutinin HA1 chain: “Crystal structure of the ivr-165 (H3N2) influenza virus hemagglutinin apo form”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 5 pockets (best druggability 0.60). MolNFT v1 #158384 on GenesisL1: 3D…
- PDB
- 6NS9
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- L0HR89
- Ligands
- NAG, BMA, MAN
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 41% strand | L0HR89 |
| B | Hemagglutinin HA2 chain | protein | 173 | 52% helix, 15% strand | L0HR89 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.60 | 0.93 | 17 | empty |
| 2 | 93 | 0.37 | 0.76 | 17 | empty |
| 3 | 56 | 0.30 | 0.75 | 17 | empty |
| 4 | 50 | 0.28 | 0.74 | 13 | empty |
| 5 | 53 | 0.24 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3050 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NS9 · Crystal structure of the IVR-165 (H3N2) influenza virus hemagglutinin apo form · 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 L0HR89
- Elsewhere: RCSB PDB 6NS9 · PDBe 6NS9 · UniProt L0HR89
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