Research workbench
SARS-cov-2 spike protein in complex with SYBODY#15 and SYBODY#68 in a 3UP conformation
Analyse SARS-cov-2 spike protein in complex with SYBODY#15 and SYBODY#68 in a 3UP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P77
- Type
- protein
- Length
- 3,822 residues
- Chains
- 9
- 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 0.80
Structure
electron microscopy · 3 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C, E | Spike glycoprotein | protein | 1036 | 20% helix, 30% strand | P0DTC2 |
| A, D, H | SYBODY#15 | protein | 114 | 3% helix, 52% strand | — |
| W, Y, X | SYBODY#68 | protein | 124 | 2% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 61 copies · chains B, C, E
- BMA · beta-D-mannopyranose · sugar · 5 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 | 461 | 0.80 | 0.87 | 67 | empty |
| 2 | 495 | 0.79 | 0.86 | 66 | empty |
| 3 | 877 | 0.78 | 0.81 | 82 | empty |
| 4 | 317 | 0.76 | 0.88 | 39 | empty |
| 5 | 377 | 0.75 | 0.86 | 54 | empty |
Interfaces
12 interfaces between chains.
- B–E · 4557 Ų buried · 39 hydrogen bonds · protein-protein
- C–E · 4516 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 4489 Ų buried · 37 hydrogen bonds · protein-protein
- E–H · 1054 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 1026 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 44 glycan (disulfide, N-glycosylation, glycosylation, O-glycosylation).
Compared structures
- 7P77 · SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 3up conformation · the same entry in another collection · chain B against B, 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 7P77 · PDBe 7P77 · UniProt P0DTC2
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