Research workbench
SARS-cov-2 delta S-8D3
Analyse SARS-cov-2 delta S-8D3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W9E
- Type
- protein
- Length
- 3,611 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain; The…
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1060 | 20% helix, 30% strand | P0DTC2 |
| D | Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain | protein | 220 | 5% helix, 44% strand | — |
| E | The light chain of 8D3 Fab | protein | 211 | 5% helix, 44% strand | — |
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 | 934 | 0.85 | 0.87 | 88 | empty |
| 2 | 822 | 0.84 | 0.87 | 112 | empty |
| 3 | 868 | 0.84 | 0.86 | 96 | empty |
| 4 | 750 | 0.81 | 0.85 | 86 | empty |
| 5 | 240 | 0.81 | 0.93 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5010 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 4600 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 4500 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1912 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 513 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide (disulfide).
Compared structures
- 7W9E · SARS-CoV-2 Delta S-8D3 · the same entry in another collection · chain B against B, 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 7W9E · PDBe 7W9E · UniProt P0DTC2
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