MolNFT v1 · #97425 · protein
Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with human receptor analog lstc
4KDO: “Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with human receptor…”. X-ray diffraction, 3 ligands (NAG, SIA, GAL), 20 pockets (best druggability 0.84). MolNFT v1 #97425 on GenesisL1: 3D…
- PDB
- 4KDO
- 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, GAL
- Pockets
- 20 · best druggability 0.84
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, 12% strand | Q6DQ33 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains C, A
- GAL · beta-D-galactopyranose · sugar · chains 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 | 631 | 0.84 | 0.88 | 89 | empty |
| 2 | 146 | 0.82 | 0.98 | 20 | empty |
| 3 | 227 | 0.82 | 0.95 | 24 | empty |
| 4 | 224 | 0.81 | 0.94 | 28 | empty |
| 5 | 216 | 0.81 | 0.95 | 28 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2858 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2801 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2767 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 1692 Ų buried · 22 hydrogen bonds · protein-protein
- D–F · 1503 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4KDO · Crystal structure of the hemagglutinin of ferret-transmissible H5N1 virus in complex with… · the same entry in another collection · chain C against C, 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 4KDO · PDBe 4KDO · UniProt Q6DQ33
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