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Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal form 1
Analyse Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S12
- Type
- protein
- Length
- 476 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q80A30
- Ligands
- NAG, SO4
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 318 | 8% helix, 40% strand | Q80A30 |
| B | Hemagglutinin HA2 chain | protein | 158 | 53% helix, 13% strand | Q80A30 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
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 | 188 | 0.58 | 0.81 | 24 | empty |
| 2 | 162 | 0.45 | 0.75 | 25 | empty |
| 3 | 68 | 0.41 | 0.80 | 15 | empty |
| 4 | 55 | 0.36 | 0.78 | 9 | empty |
| 5 | 62 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2753 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3S12 · Crystal structure of H5N1 influenza virus hemagglutinin, strain YU562 crystal form 1 · 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 Q80A30
- Elsewhere: RCSB PDB 3S12 · PDBe 3S12 · UniProt Q80A30
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