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Structure and receptor binding specificity of the hemagglutinin H13 from avian influenza a virus H13N6
Analyse Structure and receptor binding specificity of the hemagglutinin H13 from avian… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KPS
- Type
- protein
- Length
- 1,467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- P13103
- Ligands
- GAL, SIA, NAG
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin | protein | 324 | 6% helix, 41% strand | P13103 |
| B, D, F | Hemagglutinin | protein | 165 | 54% helix, 13% strand | P13103 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 766 | 0.86 | 0.90 | 109 | empty |
| 2 | 266 | 0.84 | 0.95 | 46 | empty |
| 3 | 262 | 0.76 | 0.90 | 43 | empty |
| 4 | 61 | 0.71 | 0.97 | 16 | empty |
| 5 | 248 | 0.63 | 0.81 | 43 | empty |
Interfaces
15 interfaces between chains.
- E–F · 2912 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2905 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2901 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 1242 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1228 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4KPS · Structure and receptor binding specificity of the hemagglutinin H13 from avian influenza… · 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 P13103
- Elsewhere: RCSB PDB 4KPS · PDBe 4KPS · UniProt P13103
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