MolNFT v1 · #20946 · protein
1930 swine H1 hemagglutinin complexed with lsta
1RV0: “1930 swine H1 hemagglutinin complexed with lsta”. X-ray diffraction, 2 ligands (DAN, NDG), 16 pockets (best druggability 0.87). MolNFT v1 #20946 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RV0
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q82500
- Ligands
- DAN, NDG
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J, L | Hemagglutinin | protein | 324 | 10% helix, 39% strand | Q82500 |
| I, K, M | Hemagglutinin | protein | 160 | 51% helix, 14% strand | Q82500 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains L
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.87 | 0.92 | 112 | empty |
| 2 | 365 | 0.76 | 0.87 | 53 | empty |
| 3 | 578 | 0.73 | 0.81 | 70 | empty |
| 4 | 661 | 0.71 | 0.79 | 50 | empty |
| 5 | 640 | 0.71 | 0.79 | 48 | empty |
Interfaces
15 interfaces between chains.
- J–K · 2726 Ų buried · 47 hydrogen bonds · protein-protein
- H–I · 2721 Ų buried · 47 hydrogen bonds · protein-protein
- L–M · 2684 Ų buried · 48 hydrogen bonds · protein-protein
- I–M · 1151 Ų buried · 14 hydrogen bonds · protein-protein
- I–K · 1131 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1RV0 · 1930 Swine H1 Hemagglutinin complexed with LSTA · the same entry in another collection · chain H against H, 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 Q82500
- Elsewhere: RCSB PDB 1RV0 · PDBe 1RV0 · UniProt Q82500
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.