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Crystal structure of H5N1 influenza virus hemagglutinin, clade 5
Analyse Crystal structure of H5N1 influenza virus hemagglutinin, clade 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JUN
- Type
- protein
- Length
- 1,463 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- UniProt
- Q2F4V6
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 321 | 10% helix, 41% strand | Q2F4V6 |
| B | Hemagglutinin HA2 | protein | 170 | 56% helix, 14% strand | Q2F4V6 |
| D | Hemagglutinin HA2 | protein | 164 | 52% helix, 12% strand | Q2F4V6 |
| F | Hemagglutinin HA2 | protein | 166 | 50% helix, 14% strand | Q2F4V6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.88 | 0.90 | 125 | empty |
| 2 | 64 | 0.73 | 0.98 | 15 | empty |
| 3 | 323 | 0.68 | 0.82 | 40 | empty |
| 4 | 466 | 0.67 | 0.79 | 50 | empty |
| 5 | 493 | 0.66 | 0.78 | 62 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2518 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2444 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2437 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1353 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1290 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4JUN · Crystal structure of H5N1 influenza virus hemagglutinin, clade 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 Q2F4V6
- Elsewhere: RCSB PDB 4JUN · PDBe 4JUN · UniProt Q2F4V6
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