Research workbench
Crystal structure of SARS-cov-2 spike stem helix peptide in complex with neutralizing antibody CC40.8
Analyse Crystal structure of SARS-cov-2 spike stem helix peptide in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SJS
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CC40.8 Fab heavy chain; CC40.8 Fab light chain; Stem helix peptide of spike protein S2'
- UniProt
- P0DTC2
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | CC40.8 Fab heavy chain | protein | 208 | 9% helix, 51% strand | — |
| L | CC40.8 Fab light chain | protein | 211 | 7% helix, 49% strand | — |
| C | Stem helix peptide of spike protein S2' | protein | 22 | 59% helix, 0% strand | P0DTC2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains H, C, L
- ACT · Acetate ion · additive · chains H, L
- GOL · Glycerol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.51 | 0.74 | 45 | empty |
| 2 | 83 | 0.40 | 0.78 | 16 | empty |
| 3 | 75 | 0.30 | 0.73 | 21 | empty |
| 4 | 52 | 0.30 | 0.76 | 15 | SO4 |
Interfaces
3 interfaces between chains.
- H–L · 1522 Ų buried · 12 hydrogen bonds · protein-protein
- H–C · 737 Ų buried · 6 hydrogen bonds · protein-protein
- L–C · 528 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7SJS · Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing… · 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 7SJS · PDBe 7SJS · UniProt P0DTC2
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