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Crystal structure of SARS-cov-2 receptor binding domain complexed with nanobody vhh V and antibody Fab CC12.3
Analyse Crystal structure of SARS-cov-2 receptor binding domain complexed with nanobody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KN6
- Type
- protein
- Length
- 733 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Vhh V; CC12.3 Fab heavy chain; CC12.3 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 187 | 18% helix, 28% strand | P0DTC2 |
| C | Vhh V | protein | 121 | 5% helix, 49% strand | — |
| H | CC12.3 Fab heavy chain | protein | 212 | 7% helix, 54% strand | — |
| L | CC12.3 Fab light chain | protein | 213 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.78 | 0.80 | 94 | empty |
| 2 | 280 | 0.49 | 0.73 | 45 | empty |
| 3 | 79 | 0.31 | 0.73 | 23 | empty |
| 4 | 78 | 0.30 | 0.73 | 16 | empty |
| 5 | 53 | 0.26 | 0.73 | 19 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1637 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1029 Ų buried · 23 hydrogen bonds · protein-protein
- A–H · 747 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 272 Ų buried · 5 hydrogen bonds · protein-protein
- C–L · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7KN6 · Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and… · 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 7KN6 · PDBe 7KN6 · UniProt P0DTC2
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