Research workbench
Influenza virus (VN1194) H5 ha
Analyse Influenza virus (VN1194) H5 ha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IBX
- Type
- protein
- Length
- 1,443 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q6DQ34
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 321 | 7% helix, 36% strand | Q6DQ34 |
| B, D, F | Hemagglutinin | protein | 160 | 51% helix, 14% strand | Q6DQ34 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, E, B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.88 | 0.89 | 129 | empty |
| 2 | 56 | 0.72 | 0.98 | 15 | empty |
| 3 | 978 | 0.72 | 0.76 | 98 | empty |
| 4 | 430 | 0.63 | 0.77 | 54 | empty |
| 5 | 250 | 0.61 | 0.80 | 41 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2482 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2466 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2439 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1362 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 1343 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2IBX · Influenza virus (VN1194) H5 HA · 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 Q6DQ34
- Elsewhere: RCSB PDB 2IBX · PDBe 2IBX · UniProt Q6DQ34
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.