Research workbench
Haemagglutinin of 2004 human H3N2 virus in complex with human receptor analogue lstc
Analyse Haemagglutinin of 2004 human H3N2 virus in complex with human receptor analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YP4
- Type
- protein
- Length
- 491 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- A0FCI1
- Ligands
- TAM, NAG, GAL, MAN, BGC, SIA
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 491 | 25% helix, 31% strand | A0FCI1 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar
- BGC · beta-D-glucopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.61 | 0.91 | 17 | empty |
| 2 | 134 | 0.54 | 0.81 | 27 | empty |
| 3 | 125 | 0.38 | 0.74 | 22 | empty |
Modifications
Observed in the structure: 6 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 2YP4 · Haemagglutinin of 2004 Human H3N2 Virus in Complex with Human Receptor Analogue LSTc · 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 A0FCI1
- Elsewhere: RCSB PDB 2YP4 · PDBe 2YP4 · UniProt A0FCI1
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