Research workbench
1934 H1 hemagglutinin in complex with lsta
Analyse 1934 H1 hemagglutinin in complex with lsta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RVX
- Type
- protein
- Length
- 2,896 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q82766
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Hemagglutinin | protein | 323 | 9% helix, 41% strand | Q82766 |
| B, D, H, J | Hemagglutinin | protein | 160 | 49% helix, 13% strand | Q82766 |
| F, L | Hemagglutinin | protein | 159 | 52% helix, 12% strand | Q82766 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, C, G, I, J, K, L
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, C, E, G, I, K
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, C, E, G, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.87 | 0.92 | 94 | empty |
| 2 | 278 | 0.85 | 0.96 | 35 | empty |
| 3 | 824 | 0.82 | 0.85 | 103 | empty |
| 4 | 278 | 0.74 | 0.87 | 44 | empty |
| 5 | 803 | 0.73 | 0.78 | 73 | empty |
Interfaces
30 interfaces between chains.
- E–F · 2816 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 2813 Ų buried · 46 hydrogen bonds · protein-protein
- K–L · 2790 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2790 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 2779 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide (disulfide).
Compared structures
- 1RVX · 1934 H1 Hemagglutinin in complex with LSTA · 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 Q82766
- Elsewhere: RCSB PDB 1RVX · PDBe 1RVX · UniProt Q82766
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