Research workbench
SARS-cov-2 spike protein in two-rbd weak state after ctsl-treatment
Analyse SARS-cov-2 spike protein in two-rbd weak state after ctsl-treatment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FB4
- Type
- protein
- Length
- 2,746 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 · 22% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 851 | 23% helix, 24% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 852 | 24% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1043 | 20% helix, 25% strand | P0DTC2 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.87 | 0.88 | 125 | empty |
| 2 | 795 | 0.84 | 0.87 | 111 | empty |
| 3 | 834 | 0.80 | 0.83 | 82 | empty |
| 4 | 757 | 0.78 | 0.82 | 56 | empty |
| 5 | 128 | 0.74 | 0.94 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4522 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 4149 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4095 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 7FB4 · SARS-CoV-2 spike protein in two-RBD weak state after CTSL-treatment · 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 7FB4 · PDBe 7FB4 · UniProt P0DTC2
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