Research workbench
SARS-cov-2 spike protein in complex with SYBODY#68 in a 2UP/1FLEXIBLE conformation
Analyse SARS-cov-2 spike protein in complex with SYBODY#68 in a 2UP/1FLEXIBLE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P7A
- Type
- protein
- Length
- 3,159 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; SYBODY#68
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | Spike glycoprotein | protein | 1036 | 20% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 839 | 23% helix, 31% strand | P0DTC2 |
| A, D | SYBODY#68 | protein | 124 | 2% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 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 | 902 | 0.85 | 0.87 | 117 | empty |
| 2 | 323 | 0.85 | 0.94 | 57 | empty |
| 3 | 618 | 0.82 | 0.87 | 91 | empty |
| 4 | 703 | 0.77 | 0.82 | 82 | empty |
| 5 | 1028 | 0.76 | 0.78 | 104 | empty |
Interfaces
5 interfaces between chains.
- B–C · 4565 Ų buried · 38 hydrogen bonds · protein-protein
- B–E · 4308 Ų buried · 40 hydrogen bonds · protein-protein
- C–E · 3839 Ų buried · 26 hydrogen bonds · protein-protein
- B–A · 655 Ų buried · 8 hydrogen bonds · protein-protein
- E–D · 652 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 37 disulfide (N-glycosylation, disulfide, O-glycosylation, glycosylation).
Compared structures
- 7P7A · SARS-CoV-2 spike protein in complex with sybody#68 in a 2up/1flexible 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 7P7A · PDBe 7P7A · UniProt P0DTC2
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