MolNFT v1 · #20967 · protein
1930 H1 hemagglutinin in complex with lstc
1RVT: “1930 H1 hemagglutinin in complex with lstc”. X-ray diffraction, 5 ligands (GAL, SIA, NDG), 15 pockets (best druggability 0.85). MolNFT v1 #20967 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RVT
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- GAL, SIA, NDG, BGC, NAG
- Pockets
- 15 · best druggability 0.85
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 | 9% helix, 40% strand | — |
| I, K, M | Hemagglutinin | protein | 160 | 51% helix, 14% strand | — |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains H, J, L
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains H, J, L
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains H, J, L
- BGC · beta-D-glucopyranose · sugar · chains J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.85 | 0.86 | 141 | empty |
| 2 | 88 | 0.76 | 0.98 | 16 | empty |
| 3 | 613 | 0.70 | 0.79 | 46 | empty |
| 4 | 580 | 0.70 | 0.79 | 46 | empty |
| 5 | 531 | 0.70 | 0.79 | 37 | empty |
Interfaces
15 interfaces between chains.
- H–I · 2754 Ų buried · 49 hydrogen bonds · protein-protein
- J–K · 2754 Ų buried · 48 hydrogen bonds · protein-protein
- L–M · 2725 Ų buried · 45 hydrogen bonds · protein-protein
- I–K · 1158 Ų buried · 10 hydrogen bonds · protein-protein
- I–M · 1156 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 1RVT · 1930 H1 Hemagglutinin in complex with LSTC · 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
- Elsewhere: RCSB PDB 1RVT · PDBe 1RVT
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