Research workbench
Open state of SARS-cov-2 delta variant spike protein
Analyse Open state of SARS-cov-2 delta variant spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W92
- Type
- protein
- Length
- 3,206 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1072 | 19% helix, 26% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1061 | 18% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1073 | 18% helix, 27% strand | P0DTC2 |
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 | 713 | 0.87 | 0.91 | 73 | empty |
| 2 | 943 | 0.85 | 0.86 | 107 | empty |
| 3 | 1017 | 0.83 | 0.84 | 90 | empty |
| 4 | 641 | 0.80 | 0.85 | 68 | empty |
| 5 | 969 | 0.74 | 0.77 | 91 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4597 Ų buried · 34 hydrogen bonds · protein-protein
- C–B · 4541 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 4122 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide (disulfide).
Compared structures
- 7W92 · Open state of SARS-CoV-2 Delta variant spike protein · 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 P0DTC2
- Elsewhere: RCSB PDB 7W92 · PDBe 7W92 · UniProt P0DTC2
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