Research workbench
SARS-cov-2 spike protein in complex with sybody NO68 in a 1UP/2DOWN conformation
Analyse SARS-cov-2 spike protein in complex with sybody NO68 in a 1UP/2DOWN conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P7B
- Type
- protein
- Length
- 3,207 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1069 | 19% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1071 | 18% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1067 | 18% helix, 30% strand | P0DTC2 |
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 | 689 | 0.86 | 0.90 | 88 | empty |
| 2 | 214 | 0.83 | 0.95 | 28 | empty |
| 3 | 869 | 0.82 | 0.84 | 99 | empty |
| 4 | 649 | 0.82 | 0.86 | 83 | empty |
| 5 | 549 | 0.81 | 0.87 | 76 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5365 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 5144 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 4576 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 7P7B · SARS-CoV-2 spike protein in complex with sybody no68 in a 1up/2down conformation · 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 7P7B · PDBe 7P7B · UniProt P0DTC2
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