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Crystal structure of SARS-cov-2 receptor binding domain in complex with neutralizing nanobody 17F6
Analyse Crystal structure of SARS-cov-2 receptor binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FBJ
- Type
- protein
- Length
- 2,480 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; New antigen receptor variable domain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 10 distinct chains · 10% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 199 | 18% helix, 29% strand | P0DTC2 |
| B | New antigen receptor variable domain | protein | 111 | 0% helix, 55% strand | — |
| C, O | Spike protein S1 | protein | 197 | 19% helix, 29% strand | P0DTC2 |
| D, L | New antigen receptor variable domain | protein | 112 | 0% helix, 54% strand | — |
| E | Spike protein S1 | protein | 195 | 19% helix, 30% strand | P0DTC2 |
| F | New antigen receptor variable domain | protein | 113 | 0% helix, 54% strand | — |
| G, I, K, M | Spike protein S1 | protein | 198 | 19% helix, 29% strand | P0DTC2 |
| H, J | New antigen receptor variable domain | protein | 114 | 0% helix, 54% strand | — |
| N | New antigen receptor variable domain | protein | 113 | 0% helix, 54% strand | — |
| P | New antigen receptor variable domain | protein | 111 | 0% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains G, H, I, K, M, O, A, C, E
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.68 | 0.75 | 65 | empty |
| 2 | 277 | 0.67 | 0.83 | 41 | empty |
| 3 | 430 | 0.65 | 0.79 | 54 | empty |
| 4 | 472 | 0.65 | 0.77 | 52 | empty |
| 5 | 450 | 0.65 | 0.78 | 48 | empty |
Interfaces
20 interfaces between chains.
- K–L · 740 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 715 Ų buried · 5 hydrogen bonds · protein-protein
- J–M · 713 Ų buried · 7 hydrogen bonds · protein-protein
- M–N · 710 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 692 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7FBJ · Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing… · 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 7FBJ · PDBe 7FBJ · UniProt P0DTC2
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