MolNFT v1 · #170375 · protein
Dilated form 1 of X-31 influenza haemagglutinin at pH 5 (state II)
6Y5I · X-31 influenza haemagglutinin HA1: “Dilated form 1 of X-31 influenza haemagglutinin at pH 5 (state II)”. Electron microscopy, 2 ligands (NAG, BMA), 17 pockets (best druggability 0.86). MolNFT v1 #170375 on GenesisL1: 3D structure…
- PDB
- 6Y5I
- Type
- protein
- Length
- 1,470 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-31 influenza haemagglutinin HA1; X-31 influenza haemagglutinin HA2
- UniProt
- P03437
- Ligands
- NAG, BMA
- Pockets
- 17 · best druggability 0.86
Structure
electron microscopy · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, C | X-31 influenza haemagglutinin HA1 | protein | 318 | 7% helix, 35% strand | P03437 |
| B, D, F | X-31 influenza haemagglutinin HA2 | protein | 172 | 51% helix, 11% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, E, B, D, F, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.86 | 0.88 | 87 | empty |
| 2 | 1132 | 0.86 | 0.87 | 120 | empty |
| 3 | 742 | 0.83 | 0.86 | 67 | empty |
| 4 | 543 | 0.80 | 0.87 | 56 | empty |
| 5 | 1195 | 0.75 | 0.78 | 112 | empty |
Interfaces
15 interfaces between chains.
- F–E · 2807 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2707 Ų buried · 23 hydrogen bonds · protein-protein
- D–C · 2684 Ų buried · 27 hydrogen bonds · protein-protein
- B–F · 1486 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1485 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5I · Dilated form 1 of X-31 Influenza Haemagglutinin at pH 5 (State II) · 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 P03437
- Elsewhere: RCSB PDB 6Y5I · PDBe 6Y5I · UniProt P03437
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