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Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D, N224K, Q226L and T318I) from the influenza virus A/VIET NAM/1203/2004 (H5N1)
Analyse Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N5Z
- Type
- protein
- Length
- 7,515 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin
- UniProt
- Q6DQ33
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c | Hemagglutinin HA1 chain | protein | 324 | 10% helix, 39% strand | Q6DQ33 |
| B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d | Hemagglutinin | protein | 177 | 57% helix, 12% strand | Q6DQ33 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 copies · chains A, C, K, E, G, Q, I, M, O, S, W, U, Y, c, a
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains Q, A
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 | 926 | 0.87 | 0.88 | 107 | empty |
| 2 | 353 | 0.83 | 0.92 | 61 | empty |
| 3 | 1142 | 0.83 | 0.84 | 126 | empty |
| 4 | 474 | 0.83 | 0.90 | 54 | empty |
| 5 | 845 | 0.83 | 0.85 | 110 | empty |
Interfaces
89 interfaces between chains.
- E–F · 2647 Ų buried · 36 hydrogen bonds · protein-protein
- Q–R · 2626 Ų buried · 30 hydrogen bonds · protein-protein
- c–d · 2623 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2609 Ų buried · 33 hydrogen bonds · protein-protein
- U–V · 2606 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 90 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 4N5Z · Crystal structure of aerosol transmissible influenza H5 hemagglutinin mutant (N158D… · the same entry in another collection · chain C against C, 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 Q6DQ33
- Elsewhere: RCSB PDB 4N5Z · PDBe 4N5Z · UniProt Q6DQ33
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