MolNFT v1 · #170378 · protein
Signal subtracted extended intermediate form of X-31 influenza haemagglutinin at pH 5 (state IV)
6Y5L · X-31 influenza haemagglutinin HA1,X-31 influenza…: “Signal subtracted extended intermediate form of X-31 influenza haemagglutinin at pH 5 (state IV)”. Electron microscopy, 1 ligand (NAG), 7 pockets (best druggability 0.69). MolNFT…
- PDB
- 6Y5L
- Type
- protein
- Length
- 477 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X-31 influenza haemagglutinin HA1,X-31 influenza haemagglutinin HA1; X-31 influenza…
- UniProt
- A0A286RZR2, P04663, P03437
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.69
Structure
electron microscopy · 2 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | X-31 influenza haemagglutinin HA1,X-31 influenza haemagglutinin HA1 | protein | 70 | 0% helix, 21% strand | A0A286RZR2, P04663 |
| B, D, F | X-31 influenza haemagglutinin HA2 | protein | 89 | 98% helix, 0% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.69 | 0.80 | 38 | empty |
| 2 | 88 | 0.40 | 0.77 | 20 | empty |
| 3 | 92 | 0.39 | 0.76 | 21 | empty |
| 4 | 53 | 0.33 | 0.77 | 11 | empty |
| 5 | 56 | 0.30 | 0.76 | 12 | empty |
Interfaces
9 interfaces between chains.
- D–F · 1312 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 1275 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1223 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 903 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 898 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y5L · Signal Subtracted Extended Intermediate form of X-31 Influenza Haemagglutinin at pH 5… · 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 A0A286RZR2
- Every structure of UniProt P04663
- Every structure of UniProt P03437
- Elsewhere: RCSB PDB 6Y5L · PDBe 6Y5L · UniProt A0A286RZR2 · UniProt P04663 · UniProt P03437
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