Research workbench
Crystal structure of H5 hemagglutinin from A/CHICKEN/TAIWAN/0502/2012
Analyse Crystal structure of H5 hemagglutinin from A/CHICKEN/TAIWAN/0502/2012 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YKC
- Type
- protein
- Length
- 1,488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 496 | 26% helix, 31% strand | — |
| B | Hemagglutinin | protein | 497 | 26% helix, 29% strand | — |
| C | Hemagglutinin | protein | 495 | 24% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.83 | 0.84 | 73 | empty |
| 2 | 52 | 0.71 | 0.98 | 14 | empty |
| 3 | 297 | 0.69 | 0.84 | 39 | empty |
| 4 | 121 | 0.68 | 0.89 | 31 | empty |
| 5 | 444 | 0.64 | 0.77 | 53 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2223 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2193 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2165 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 11 disulfide (N-glycosylation, disulfide).
Compared structures
- 5YKC · crystal structure of H5 hemagglutinin from A/chicken/Taiwan/0502/2012 · 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
- Elsewhere: RCSB PDB 5YKC · PDBe 5YKC
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