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Crystal structure of a H5N1 influenza virus hemagglutinin from A/GOOSE/GUANGDONG/1/96
Analyse Crystal structure of a H5N1 influenza virus hemagglutinin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MHI
- Type
- protein
- Length
- 4,464 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q9Q0U6
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q | Hemagglutinin HA1 chain | protein | 323 | 10% helix, 40% strand | Q9Q0U6 |
| B, D, F, H, J, L, N, P, R | Hemagglutinin HA2 chain | protein | 173 | 56% helix, 13% strand | Q9Q0U6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, E, C, G, I, K, M, Q, O, R
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.88 | 0.89 | 130 | empty |
| 2 | 1195 | 0.87 | 0.89 | 137 | empty |
| 3 | 550 | 0.82 | 0.87 | 65 | empty |
| 4 | 92 | 0.78 | 0.98 | 15 | empty |
| 5 | 78 | 0.76 | 0.99 | 15 | empty |
Interfaces
47 interfaces between chains.
- E–F · 2589 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2537 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2512 Ų buried · 36 hydrogen bonds · protein-protein
- M–N · 2510 Ų buried · 45 hydrogen bonds · protein-protein
- Q–R · 2510 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 disulfide, 22 glycan (disulfide, N-glycosylation).
Compared structures
- 4MHI · Crystal structure of a H5N1 influenza virus hemagglutinin from A/goose/Guangdong/1/96 · 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 Q9Q0U6
- Elsewhere: RCSB PDB 4MHI · PDBe 4MHI · UniProt Q9Q0U6
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