MolNFT v1 · #110244 · protein
Crystal structure of hemagglutinin from jiangxi-donghu (2013) H10N8 influenza virus in complex with 6'-sln
4XQO · Hemagglutinin HA1 chain: “Crystal structure of hemagglutinin from jiangxi-donghu (2013) H10N8 influenza virus in complex with 6'-sln”. X-ray diffraction, 3 ligands (NAG, GAL, SIA), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 4XQO
- Type
- protein
- Length
- 1,452 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain
- UniProt
- A0A059T4A1
- Ligands
- NAG, GAL, SIA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 316 | 8% helix, 40% strand | A0A059T4A1 |
| B | Hemagglutinin HA2 chain | protein | 169 | 59% helix, 11% strand | A0A059T4A1 |
| C | Hemagglutinin HA1 chain | protein | 315 | 7% helix, 38% strand | A0A059T4A1 |
| D | Hemagglutinin HA2 chain | protein | 168 | 58% helix, 5% strand | A0A059T4A1 |
| E | Hemagglutinin HA1 chain | protein | 318 | 9% helix, 40% strand | A0A059T4A1 |
| F | Hemagglutinin HA2 chain | protein | 166 | 60% helix, 7% strand | A0A059T4A1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, E, C, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.85 | 0.97 | 24 | empty |
| 2 | 402 | 0.84 | 0.92 | 47 | empty |
| 3 | 697 | 0.76 | 0.81 | 85 | empty |
| 4 | 81 | 0.74 | 0.97 | 20 | empty |
| 5 | 78 | 0.72 | 0.96 | 18 | empty |
Interfaces
15 interfaces between chains.
- E–F · 3133 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 3084 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2861 Ų buried · 25 hydrogen bonds · protein-protein
- D–F · 1715 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1579 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4XQO · Crystal structure of hemagglutinin from Jiangxi-Donghu (2013) H10N8 influenza virus in… · the same entry in another collection · chain B against B, 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 A0A059T4A1
- Elsewhere: RCSB PDB 4XQO · PDBe 4XQO · UniProt A0A059T4A1
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