Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in a ternary complex with covox-88 and covox-45 fabs
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BEL
- Type
- protein
- Length
- 1,728 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-45 heavy chain; Covox-88 heavy chain; Covox-88 light chain…
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R, X | Spike glycoprotein | protein | 194 | 15% helix, 30% strand | P0DTC2 |
| A, C | Covox-45 heavy chain | protein | 216 | 6% helix, 50% strand | — |
| H, E | Covox-88 heavy chain | protein | 128 | 7% helix, 48% strand | — |
| L, F | Covox-88 light chain | protein | 113 | 3% helix, 47% strand | — |
| B, D | Covox-45 light chain | protein | 213 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains R, H, X, E
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains R, X, F
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains R, X
- ACT · Acetate ion · additive · 3 copies · chains R, A, X, C
- GOL · Glycerol · additive · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.65 | 0.78 | 67 | NAG |
| 2 | 437 | 0.63 | 0.77 | 64 | NAG |
| 3 | 153 | 0.63 | 0.85 | 34 | empty |
| 4 | 112 | 0.59 | 0.86 | 25 | empty |
| 5 | 469 | 0.58 | 0.74 | 55 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1669 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1622 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 859 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 850 Ų buried · 10 hydrogen bonds · protein-protein
- R–A · 798 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7BEL · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a… · the same entry in another collection · chain R against R, 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 7BEL · PDBe 7BEL · UniProt P0DTC2
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