MolNFT v1 · #55598 · protein
Haemagglutinin of 1968 human H3N2 virus in complex with human receptor analogue lstc
2YPG · Hemagglutinin HA1 chain: “Haemagglutinin of 1968 human H3N2 virus in complex with human receptor analogue lstc”. X-ray diffraction, 6 ligands (NAG, GAL, BMA), 19 pockets (best druggability 0.87). MolNFT v1 #55598 on GenesisL1: 3D…
- 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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