Research workbench
Structures of monomeric hemagglutinin and its complex with an Fab fragment of a neutralizing antibody that binds to H1 subtype influenza viruses: molecular basis of infectivity of 2009 pandemic H1N1 influenza a viruses
Analyse Structures of monomeric hemagglutinin and its complex with an Fab fragment of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EDB
- Type
- protein
- Length
- 1,449 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A7LI25
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 323 | 6% helix, 29% strand | A7LI25 |
| B, D, F | Hemagglutinin | protein | 160 | 43% helix, 8% strand | A7LI25 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.84 | 0.96 | 31 | empty |
| 2 | 1134 | 0.82 | 0.83 | 119 | empty |
| 3 | 149 | 0.79 | 0.96 | 25 | empty |
| 4 | 749 | 0.76 | 0.81 | 97 | empty |
| 5 | 106 | 0.75 | 0.95 | 23 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2972 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 2794 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 2739 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1528 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1518 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 4EDB · Structures of monomeric hemagglutinin and its complex with an Fab fragment of a… · 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 A7LI25
- Elsewhere: RCSB PDB 4EDB · PDBe 4EDB · UniProt A7LI25
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