Research workbench
Haemagglutinin of 1968 human H3N2 virus in complex with human receptor analogue lstc
Analyse Haemagglutinin of 1968 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
- 2YPG
- Type
- protein
- Length
- 1,473 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- P03437
- Ligands
- NAG, GAL, BMA, SIA, BGC, FUL
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 39% strand | P03437 |
| B, F | Hemagglutinin HA2 chain | protein | 173 | 53% helix, 14% strand | P03437 |
| C | Hemagglutinin HA1 chain | protein | 320 | 10% helix, 39% strand | P03437 |
| D | Hemagglutinin HA2 chain | protein | 172 | 53% helix, 15% strand | P03437 |
| E | Hemagglutinin HA1 chain | protein | 318 | 10% helix, 40% strand | P03437 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, E, B, C, D, F
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains E, A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, E
- FUL · beta-L-fucopyranose · sugar · chains A
- FLC · Citrate anion · additive · 13 copies · chains A, B, D, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.87 | 0.88 | 104 | FLC |
| 2 | 266 | 0.84 | 0.95 | 32 | empty |
| 3 | 302 | 0.71 | 0.84 | 23 | FLC |
| 4 | 477 | 0.71 | 0.81 | 51 | FLC |
| 5 | 432 | 0.70 | 0.81 | 50 | empty |
Interfaces
15 interfaces between chains.
- C–D · 3065 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 3059 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 3021 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 1553 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1524 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 15 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 2YPG · Haemagglutinin of 1968 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 P03437
- Elsewhere: RCSB PDB 2YPG · PDBe 2YPG · UniProt P03437
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