Research workbench
Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2 receptor binding domain
Analyse Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KLW
- Type
- protein
- Length
- 441 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Severe acute respiratory syndrome coronavirus 2; synthetic construct
- Molecule
- Spike protein S1; SB45, Synthetic Nanobody; SB68, Synthetic nanobody
- UniProt
- P0DTC2
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 18% helix, 30% strand | P0DTC2 |
| B | SB45, Synthetic Nanobody | protein | 120 | 5% helix, 54% strand | — |
| C | SB68, Synthetic nanobody | protein | 127 | 5% helix, 51% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.52 | 0.78 | 31 | empty |
| 2 | 63 | 0.51 | 0.86 | 15 | empty |
| 3 | 87 | 0.34 | 0.74 | 17 | empty |
| 4 | 73 | 0.32 | 0.74 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1074 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 668 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7KLW · Crystal structure of synthetic nanobody (SB45+SB68) complexes with SARS-cov-2 receptor… · 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 7KLW · PDBe 7KLW · UniProt P0DTC2
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