MolNFT v1 · #137610 · protein
Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant in complex with 3'-sln
5VTY · Hemagglutinin HA1 chain: “Crystal structure of the A/HONG KONG/1/1968 (H3N2) influenza virus hemagglutinin G225Q/L226A mutant in…”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 16 pockets (best druggability 0.87). MolNFT v1 #137610…
- PDB
- 5VTY
- Type
- protein
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- Q91MA7
- Ligands
- NAG, MAN, BMA, GAL, SIA
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 316 | 10% helix, 43% strand | Q91MA7 |
| B, D, F | Hemagglutinin HA2 chain | protein | 171 | 54% helix, 15% strand | Q91MA7 |
| C | Hemagglutinin HA1 chain | protein | 317 | 10% helix, 43% strand | Q91MA7 |
| E | Hemagglutinin HA1 chain | protein | 321 | 10% helix, 42% strand | Q91MA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A, C, B, E, D, F
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, E
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, E, A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, C, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.87 | 0.90 | 39 | empty |
| 2 | 455 | 0.85 | 0.92 | 55 | empty |
| 3 | 253 | 0.75 | 0.89 | 31 | empty |
| 4 | 818 | 0.74 | 0.79 | 89 | empty |
| 5 | 245 | 0.73 | 0.87 | 30 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2997 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2970 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2927 Ų buried · 46 hydrogen bonds · protein-protein
- B–F · 1506 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1500 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 5VTY · Crystal structure of the A/Hong Kong/1/1968 (H3N2) influenza virus hemagglutinin… · the same entry in another collection · chain C against C, 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 Q91MA7
- Elsewhere: RCSB PDB 5VTY · PDBe 5VTY · UniProt Q91MA7
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