MolNFT v2 · #225523 · protein
3up-TM conformation of HKU1-B S protein after incubation of the receptor
8Y1E · Spike glycoprotein: “3up-TM conformation of HKU1-B S protein after incubation of the receptor”. Electron microscopy at 2.7, 2 ligands (NAG, MAN), 20 pockets (best druggability 0.88). MolNFT v2 #225523 on GenesisL1: 3D structure…
- PDB
- 8Y1E
- Type
- protein
- Length
- 4,659 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens; Human coronavirus HKU1 (isolate N2)
- Molecule
- Spike glycoprotein; Transmembrane protease serine 2
- EC
- 3.4.21.122
- UniProt
- Q14EB0, O15393
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · resolution 2.7 · 2 distinct chains · 17% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1208 | 20% helix, 29% strand | Q14EB0 |
| D, E, F | Transmembrane protease serine 2 (EC 3.4.21.122) | protein | 345 | 7% helix, 24% strand | O15393 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 12 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.88 | 0.90 | 104 | empty |
| 2 | 651 | 0.84 | 0.89 | 64 | empty |
| 3 | 646 | 0.82 | 0.86 | 65 | empty |
| 4 | 1072 | 0.81 | 0.83 | 96 | empty |
| 5 | 121 | 0.78 | 0.96 | 33 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4542 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4459 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4340 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 885 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 885 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 90 disulfide, 66 glycan (disulfide, N-glycosylation).
Compared structures
- O15393 · AlphaFold monomer V2.0 prediction for transmembrane protease serine 2 (O15393) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 Q14EB0
- Every structure of UniProt O15393
- Elsewhere: RCSB PDB 8Y1E · PDBe 8Y1E · UniProt Q14EB0 · UniProt O15393
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