Research workbench
H5 (tyty) influenza virus haemagglutinin in complex with avian receptor analogue 3'-sln
Analyse H5 (tyty) influenza virus 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
- 4BH1
- Type
- protein
- Length
- 1,393 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q207Z6
- Ligands
- NAG, GAL, SIA, PO4
- Pockets
- 17 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 319 | 10% helix, 41% strand | Q207Z6 |
| B, F | Hemagglutinin | protein | 145 | 53% helix, 8% strand | Q207Z6 |
| D | Hemagglutinin | protein | 146 | 55% helix, 8% strand | Q207Z6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 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 · 4 copies · chains A, 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 | 848 | 0.71 | 0.76 | 92 | empty |
| 2 | 869 | 0.70 | 0.76 | 89 | PO4 |
| 3 | 559 | 0.65 | 0.76 | 64 | empty |
| 4 | 389 | 0.64 | 0.78 | 46 | empty |
| 5 | 446 | 0.59 | 0.75 | 40 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2256 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2217 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2195 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 969 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 916 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4BH1 · H5 (tyTy) Influenza Virus Haemagglutinin in Complex with Avian Receptor Analogue 3'-SLN · the same entry in another collection · chain B against B, 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 4BH1 · PDBe 4BH1 · UniProt Q207Z6
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