Research workbench
Human coronavirus HKU1 haemagglutinin-esterase
Analyse Human coronavirus HKU1 haemagglutinin-esterase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y3Y
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin-esterase
- EC
- 3.1.1.53
- UniProt
- Q5MQD1
- Ligands
- NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 14% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemagglutinin-esterase (EC 3.1.1.53) | protein | 332 | 14% helix, 26% strand | Q5MQD1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.70 | 0.95 | 16 | empty |
| 2 | 1010 | 0.70 | 0.74 | 60 | empty |
| 3 | 75 | 0.33 | 0.75 | 15 | empty |
| 4 | 73 | 0.33 | 0.75 | 17 | empty |
| 5 | 86 | 0.31 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1438 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6Y3Y · Human Coronavirus HKU1 Haemagglutinin-Esterase · 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 Q5MQD1
- Elsewhere: RCSB PDB 6Y3Y · PDBe 6Y3Y · UniProt Q5MQD1
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