Research workbench
SARS-cov-2 receptor-binding domain speedesign immunogen 1 bound to C144 scfv
Analyse SARS-cov-2 receptor-binding domain speedesign immunogen 1 bound to C144 scfv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DCE
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C144 scfv; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | C144 scfv | protein | 242 | 4% helix, 47% strand | — |
| A | Spike protein S1 | protein | 194 | 18% helix, 31% strand | P0DTC2 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.59 | 0.76 | 44 | empty |
| 2 | 115 | 0.37 | 0.74 | 29 | empty |
Interfaces
1 interface between chains.
- H–A · 844 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 8DCE · SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv · the same entry in another collection · chain H against H, 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 8DCE · PDBe 8DCE · UniProt P0DTC2
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