Research workbench
H5 (tyty) DEL133/ILE155THR mutant haemagglutinin in complex with avian receptor analogue lsta
Analyse H5 (tyty) DEL133/ILE155THR mutant haemagglutinin in complex with avian receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CQY
- Type
- protein
- Length
- 1,458 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haemagglutinin HA1; Haemagglutinin HA2
- UniProt
- Q207Z6
- Ligands
- NAG, GAL, SIA, PO4
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haemagglutinin HA1 | protein | 324 | 10% helix, 41% strand | Q207Z6 |
| B, D | Haemagglutinin HA2 | protein | 163 | 55% helix, 15% strand | Q207Z6 |
| C, E | Haemagglutinin HA1 | protein | 322 | 10% helix, 41% strand | Q207Z6 |
| F | Haemagglutinin HA2 | protein | 164 | 54% helix, 13% strand | Q207Z6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, E, C
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- PO4 · Phosphate ion · ion · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.81 | 0.83 | 100 | empty |
| 2 | 375 | 0.80 | 0.89 | 73 | empty |
| 3 | 55 | 0.73 | 0.99 | 15 | empty |
| 4 | 386 | 0.64 | 0.78 | 48 | empty |
| 5 | 347 | 0.64 | 0.79 | 55 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2607 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2549 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2524 Ų buried · 41 hydrogen bonds · protein-protein
- B–F · 1322 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1300 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 4CQY · H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin in Complex with Avian Receptor Analogue… · 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 Q207Z6
- Elsewhere: RCSB PDB 4CQY · PDBe 4CQY · UniProt Q207Z6
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