MolNFT v1 · #187793 · protein
C98C7 Fab in complex with SARS-cov-2 spike 6P (rbd local reconstruction)
7SWO · Spike protein S1: “C98C7 Fab in complex with SARS-cov-2 spike 6P (rbd local reconstruction)”. Electron microscopy, 9 pockets (best druggability 0.62). MolNFT v1 #187793 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SWO
- Type
- protein
- Length
- 627 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; C98C7 Fab heavy chain; C98C7 Fab light chain
- UniProt
- P0DTC2
- Pockets
- 9 · best druggability 0.62
Structure
electron microscopy · 3 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 195 | 13% helix, 22% strand | P0DTC2 |
| H | C98C7 Fab heavy chain | protein | 219 | 7% helix, 50% strand | — |
| L | C98C7 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.62 | 0.86 | 36 | empty |
| 2 | 77 | 0.59 | 0.89 | 23 | empty |
| 3 | 391 | 0.58 | 0.75 | 49 | empty |
| 4 | 120 | 0.44 | 0.77 | 20 | empty |
| 5 | 92 | 0.42 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1720 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 818 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 554 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7SWO · C98C7 Fab in complex with SARS-CoV-2 Spike 6P (RBD local reconstruction) · 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 7SWO · PDBe 7SWO · UniProt P0DTC2
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