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
- 7WGB
- Type
- protein
- Length
- 4,482 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Processed angiotensin-converting enzyme 2
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1098 | 21% helix, 27% strand | P0DTC2 |
| D, F | Processed angiotensin-converting enzyme 2 | protein | 594 | 58% helix, 3% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 76 copies · chains A, B, C, D, F
- BMA · beta-D-mannopyranose · sugar · 5 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 | 1136 | 0.87 | 0.88 | 125 | empty |
| 2 | 1111 | 0.87 | 0.88 | 87 | empty |
| 3 | 818 | 0.80 | 0.83 | 94 | empty |
| 4 | 442 | 0.80 | 0.88 | 50 | empty |
| 5 | 729 | 0.80 | 0.84 | 78 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4915 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 4326 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 4144 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 995 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 954 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 45 disulfide (disulfide, N-glycosylation, glycosylation, O-glycosylation, glycation).
Compared structures
- 7WGB · 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 F against A, TM-score 0.96
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.96
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.96
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.96
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F 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 P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7WGB · PDBe 7WGB · UniProt P0DTC2 · UniProt Q9BYF1
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