Research workbench
SARS-cov-2 spike protein in complex with SYBODY#15 and SYBODY#68 in a 1UP/1UP-OUT/1DOWN conformation
Analyse SARS-cov-2 spike protein in complex with SYBODY#15 and SYBODY#68 in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P78
- Type
- protein
- Length
- 3,625 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; SYBODY#15; SYBODY#68
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | Spike glycoprotein | protein | 1036 | 20% helix, 28% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 963 | 22% helix, 30% strand | P0DTC2 |
| B, D, H | SYBODY#15 | protein | 114 | 5% helix, 49% strand | — |
| W, Y | SYBODY#68 | protein | 124 | 5% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains A, C, E
- BMA · beta-D-mannopyranose · sugar · 4 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 787 | 0.85 | 0.88 | 103 | empty |
| 2 | 669 | 0.82 | 0.86 | 97 | empty |
| 3 | 187 | 0.80 | 0.95 | 37 | empty |
| 4 | 319 | 0.79 | 0.90 | 38 | empty |
| 5 | 772 | 0.78 | 0.82 | 80 | empty |
Interfaces
11 interfaces between chains.
- C–A · 4637 Ų buried · 40 hydrogen bonds · protein-protein
- E–A · 4518 Ų buried · 42 hydrogen bonds · protein-protein
- C–E · 4008 Ų buried · 35 hydrogen bonds · protein-protein
- E–H · 1007 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1001 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 33 glycan (disulfide, N-glycosylation, O-glycosylation, glycosylation).
Compared structures
- 7P78 · SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 1up/1up-out/1down… · the same entry in another collection · chain C against C, 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 7P78 · PDBe 7P78 · UniProt P0DTC2
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