Research workbench
Crystal structure of a subtype H18 hemagglutinin homologue from A/FLAT-faced BAT/PERU/033/2010 (H18N11)
Analyse Crystal structure of a subtype H18 hemagglutinin homologue from A/FLAT-faced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K3X
- Type
- protein
- Length
- 1,476 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2
- Ligands
- P4G, NAG, FUL, MAN, BMA, FUC
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 322 | 8% helix, 41% strand | — |
| B, D, F | Hemagglutinin HA2 | protein | 170 | 59% helix, 14% strand | — |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 12 copies · chains A, C, D, F, E, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains A, B, C, D, E, F
- FUL · beta-L-fucopyranose · sugar · 8 copies · chains A, B, D, C, F
- MAN · alpha-D-mannopyranose · sugar · 6 copies
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.87 | 0.97 | 34 | empty |
| 2 | 835 | 0.85 | 0.87 | 63 | empty |
| 3 | 946 | 0.74 | 0.77 | 116 | P4G |
| 4 | 905 | 0.74 | 0.78 | 98 | empty |
| 5 | 184 | 0.67 | 0.86 | 36 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2972 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2954 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2926 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 1446 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1434 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 4K3X · Crystal structure of a subtype H18 hemagglutinin homologue from A/flat-faced… · 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
- Elsewhere: RCSB PDB 4K3X · PDBe 4K3X
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