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Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with avian receptor analog lsta
Analyse Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KDN
- Type
- protein
- Length
- 1,491 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q6DQ33
- Ligands
- NAG, SIA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 322 | 7% helix, 41% strand | Q6DQ33 |
| B, D, F | Hemagglutinin | protein | 175 | 59% helix, 13% strand | Q6DQ33 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 726 | 0.85 | 0.88 | 99 | empty |
| 2 | 174 | 0.84 | 0.98 | 23 | empty |
| 3 | 224 | 0.81 | 0.94 | 27 | empty |
| 4 | 226 | 0.81 | 0.94 | 26 | empty |
| 5 | 219 | 0.81 | 0.94 | 24 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2839 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2811 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2764 Ų buried · 36 hydrogen bonds · protein-protein
- B–F · 1700 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1540 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4KDN · Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with… · the same entry in another collection · chain D against D, 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 Q6DQ33
- Elsewhere: RCSB PDB 4KDN · PDBe 4KDN · UniProt Q6DQ33
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