Research workbench
Haemagglutinin of 2005 human H3N2 virus in complex with avian receptor analogue 3SLN
Analyse Haemagglutinin of 2005 human H3N2 virus in complex with avian receptor analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YP9
- Type
- protein
- Length
- 490 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- I2D7A8
- Ligands
- TAM, NAG, MAN, SIA, CMO
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 490 | 25% helix, 31% strand | I2D7A8 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- CMO · Carbon monoxide · ion
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.59 | 0.92 | 17 | empty |
| 2 | 54 | 0.57 | 0.91 | 16 | empty |
| 3 | 174 | 0.42 | 0.74 | 29 | empty |
| 4 | 59 | 0.33 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 7 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 2YP9 · Haemagglutinin of 2005 Human H3N2 Virus in Complex with Avian Receptor Analogue 3SLN · 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 I2D7A8
- Elsewhere: RCSB PDB 2YP9 · PDBe 2YP9 · UniProt I2D7A8
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