Research workbench
Neutral omicron spike trimer in complex with ACE2.
Analyse Neutral omicron spike trimer in complex with ACE2. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WGC
- Type
- protein
- Length
- 795 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike glycoprotein
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 46% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 594 | 59% helix, 2% strand | Q9BYF1 |
| C | Spike glycoprotein | protein | 201 | 7% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.79 | 0.97 | 30 | empty |
| 2 | 1157 | 0.74 | 0.77 | 104 | empty |
| 3 | 483 | 0.69 | 0.79 | 46 | empty |
| 4 | 58 | 0.64 | 0.93 | 20 | empty |
| 5 | 150 | 0.59 | 0.83 | 24 | empty |
Interfaces
1 interface between chains.
- A–C · 979 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7WGC · Neutral Omicron Spike Trimer in complex with ACE2. · the same entry in another collection · chain C against C, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7WGC · PDBe 7WGC · UniProt Q9BYF1 · UniProt P0DTC2
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