Research workbench
SARS-cov-2 beta spike SD1 in complex with S3H3 Fab
Analyse SARS-cov-2 beta spike SD1 in complex with S3H3 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WD8
- Type
- protein
- Length
- 524 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of S3H3 Fab; Light chain of S3H3 Fab
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.52
Structure
electron microscopy · 4 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 20 | 0% helix, 25% strand | P0DTC2 |
| E | Heavy chain of S3H3 Fab | protein | 217 | 1% helix, 52% strand | — |
| F | Light chain of S3H3 Fab | protein | 215 | 6% helix, 50% strand | — |
| B | Spike glycoprotein | protein | 72 | 6% helix, 39% strand | P0DTC2 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 348 | 0.52 | 0.73 | 46 | empty |
| 2 | 185 | 0.44 | 0.74 | 27 | empty |
| 3 | 111 | 0.39 | 0.75 | 20 | empty |
| 4 | 75 | 0.32 | 0.74 | 15 | empty |
| 5 | 65 | 0.32 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- E–F · 1808 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1088 Ų buried · 16 hydrogen bonds · protein-protein
- E–B · 479 Ų buried · 4 hydrogen bonds · protein-protein
- F–B · 334 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 161 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7WD8 · SARS-CoV-2 Beta spike SD1 in complex with S3H3 Fab · 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 7WD8 · PDBe 7WD8 · UniProt P0DTC2
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