MolNFT v1 · #173903 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-158 Fab (crystal form 2)
7BEK · Covox-158 heavy chain: “Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-158…”. X-ray diffraction, 4 ligands (NAG, FUC, CL), 8 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 7BEK
- Type
- protein
- Length
- 628 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-158 heavy chain; Covox-158 light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, CL, SO4
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Covox-158 heavy chain | protein | 220 | 8% helix, 51% strand | — |
| L | Covox-158 light chain | protein | 214 | 6% helix, 51% strand | — |
| E | Spike glycoprotein | protein | 194 | 18% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · 6 copies · chains H, L, E
- SO4 · Sulfate ion · ion · 2 copies · chains H, E, L
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains H, E, L
- GOL · Glycerol · additive · 3 copies · chains H, L, E
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains H, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.64 | 0.88 | 29 | TRS |
| 2 | 357 | 0.62 | 0.78 | 39 | PEG, CL |
| 3 | 293 | 0.52 | 0.74 | 40 | empty |
| 4 | 160 | 0.47 | 0.76 | 28 | empty |
| 5 | 57 | 0.34 | 0.78 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1798 Ų buried · 21 hydrogen bonds · protein-protein
- H–E · 682 Ų buried · 13 hydrogen bonds · protein-protein
- L–E · 558 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7BEK · 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 7BEK · PDBe 7BEK · UniProt P0DTC2
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