Research workbench
H5 (VN1194) influenza virus haemagglutinin in complex with avian receptor analogue 3'-sln
Analyse H5 (VN1194) 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
- 4BGY
- Type
- protein
- Length
- 483 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q6DQ34
- Ligands
- NAG, GAL, SIA
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 321 | 9% helix, 42% strand | Q6DQ34 |
| B | Hemagglutinin | protein | 162 | 54% helix, 14% strand | Q6DQ34 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.60 | 0.77 | 48 | empty |
| 2 | 53 | 0.39 | 0.81 | 14 | empty |
| 3 | 53 | 0.36 | 0.79 | 13 | empty |
| 4 | 55 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2438 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4BGY · H5 (VN1194) Influenza Virus Haemagglutinin in Complex with Avian Receptor Analogue 3'-SLN · 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 Q6DQ34
- Elsewhere: RCSB PDB 4BGY · PDBe 4BGY · UniProt Q6DQ34
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