MolNFT v1 · #173905 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-269 scfv
7BEM · Covox-269 vh domain: “Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-269…”. X-ray diffraction, 5 ligands (PRO, NAG, FUC), 4 pockets (best druggability 0.70). MolNFT v1 #173905…
- PDB
- 7BEM
- Type
- protein
- Length
- 413 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-269 vh domain; Covox-269 vl domain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- PRO, NAG, FUC, CL, PO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Covox-269 vh domain | protein | 117 | 8% helix, 53% strand | — |
| L | Covox-269 vl domain | protein | 110 | 3% helix, 49% strand | — |
| E | Spike glycoprotein | protein | 186 | 17% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- PRO · Proline · ligand · 4 copies · chains E, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · 2 copies · chains H, E
- PO4 · Phosphate ion · ion · 2 copies · chains L, H, E
- GOL · Glycerol · additive · 2 copies · chains H, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.70 | 0.89 | 28 | GOL |
| 2 | 51 | 0.35 | 0.79 | 15 | empty |
| 3 | 67 | 0.30 | 0.73 | 18 | PO4 |
| 4 | 61 | 0.27 | 0.73 | 10 | empty |
Interfaces
3 interfaces between chains.
- H–E · 857 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 771 Ų buried · 10 hydrogen bonds · protein-protein
- L–E · 507 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7BEM · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · the same entry in another collection · chain H against H, 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 7BEM · PDBe 7BEM · UniProt P0DTC2
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