Research workbench
Insight into highly conserved H1 subtype-specific epitopes in influenza virus hemagglutinin
Analyse Insight into highly conserved H1 subtype-specific epitopes in influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LVH
- Type
- protein
- Length
- 2,613 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Monoclonal antibody H-chain; Monoclonal antibody L-chain
- UniProt
- C5MQE6
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 236 | 8% helix, 26% strand | C5MQE6 |
| B, E, H, K | Monoclonal antibody H-chain | protein | 218 | 3% helix, 35% strand | — |
| C, F, I | Monoclonal antibody L-chain | protein | 210 | 2% helix, 33% strand | — |
| D, G, J | Hemagglutinin | protein | 222 | 11% helix, 30% strand | C5MQE6 |
| L | Monoclonal antibody L-chain | protein | 209 | 4% helix, 30% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.79 | 0.90 | 48 | empty |
| 2 | 265 | 0.76 | 0.88 | 42 | empty |
| 3 | 638 | 0.70 | 0.78 | 73 | empty |
| 4 | 202 | 0.68 | 0.86 | 32 | empty |
| 5 | 726 | 0.66 | 0.75 | 71 | empty |
Interfaces
17 interfaces between chains.
- E–F · 1851 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1761 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1718 Ų buried · 11 hydrogen bonds · protein-protein
- K–L · 1698 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 734 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 4LVH · Insight into highly conserved H1 subtype-specific epitopes in influenza virus… · 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 C5MQE6
- Elsewhere: RCSB PDB 4LVH · PDBe 4LVH · UniProt C5MQE6
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