MolNFT v1 · #98024 · protein
Structure of A/ANHUI/5/2005 H5 ha
4KWM · Hemagglutinin: “Structure of A/ANHUI/5/2005 H5 ha”. X-ray diffraction, 1 ligand (NAG), 18 pockets (best druggability 0.70). MolNFT v1 #98024 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4KWM
- Type
- protein
- Length
- 1,459 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- C0LYC6
- Ligands
- NAG
- Pockets
- 18 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 323 | 8% helix, 37% strand | C0LYC6 |
| B, D, F | Hemagglutinin | protein | 164 | 55% helix, 13% strand | C0LYC6 |
| C, E | Hemagglutinin | protein | 322 | 8% helix, 39% strand | C0LYC6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.70 | 0.79 | 54 | empty |
| 2 | 418 | 0.63 | 0.77 | 53 | empty |
| 3 | 253 | 0.61 | 0.80 | 27 | empty |
| 4 | 256 | 0.61 | 0.80 | 29 | empty |
| 5 | 156 | 0.57 | 0.82 | 25 | empty |
Interfaces
6 interfaces between chains.
- E–F · 2631 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2616 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2548 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 246 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4KWM · Structure of a/anhui/5/2005 h5 ha · 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 C0LYC6
- Elsewhere: RCSB PDB 4KWM · PDBe 4KWM · UniProt C0LYC6
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