MolNFT v1 · #117267 · protein
Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/DUCK/EGYPT/10185SS/2010 (H5N1)
5E2Y: “Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/DUCK/EGYPT/10185SS/2010 (H5N1)”. X-ray diffraction, 3 ligands (NAG, FUL, FUC), 14 pockets (best druggability 0.85). MolNFT v1 #117267 on GenesisL1: 3D…
- PDB
- 5E2Y
- Type
- protein
- Length
- 1,494 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- G8IPF0
- Ligands
- NAG, FUL, FUC
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 323 | 10% helix, 41% strand | G8IPF0 |
| B, D, F | Hemagglutinin | protein | 175 | 55% helix, 12% strand | G8IPF0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
- FUL · beta-L-fucopyranose · sugar · 3 copies · chains A, C, E
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.85 | 0.88 | 105 | empty |
| 2 | 371 | 0.83 | 0.92 | 51 | empty |
| 3 | 71 | 0.76 | 0.99 | 15 | empty |
| 4 | 937 | 0.72 | 0.76 | 97 | empty |
| 5 | 689 | 0.66 | 0.75 | 77 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2557 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2543 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2532 Ų buried · 40 hydrogen bonds · protein-protein
- D–F · 1404 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 1385 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5E2Y · Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus… · 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 G8IPF0
- Elsewhere: RCSB PDB 5E2Y · PDBe 5E2Y · UniProt G8IPF0
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