MolNFT v1 · #97423 · protein
Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
4KDM: “Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #97423 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KDM
- 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
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 322 | 7% helix, 38% strand | Q6DQ33 |
| B, D, F | Hemagglutinin | protein | 175 | 56% helix, 14% strand | Q6DQ33 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, E
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 | 880 | 0.87 | 0.89 | 119 | empty |
| 2 | 156 | 0.82 | 0.98 | 21 | empty |
| 3 | 231 | 0.82 | 0.94 | 30 | empty |
| 4 | 221 | 0.81 | 0.94 | 25 | empty |
| 5 | 239 | 0.80 | 0.93 | 29 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2819 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2812 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2781 Ų buried · 34 hydrogen bonds · protein-protein
- B–F · 1696 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1624 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4KDM · Crystal structure of the hemagglutinin of ferret-transmissible H5N1 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 Q6DQ33
- Elsewhere: RCSB PDB 4KDM · PDBe 4KDM · UniProt Q6DQ33
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