MolNFT v1 · #173900 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-316 Fab
7BEH: “Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-316…”. X-ray diffraction, 2 ligands (NAG, FUC), 5 pockets (best druggability 0.71). MolNFT v1 #173900 on GenesisL1: 3D…
- PDB
- 7BEH
- Type
- protein
- Length
- 626 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-316 heavy chain; Covox-316 light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike glycoprotein | protein | 195 | 12% helix, 29% strand | P0DTC2 |
| H | Covox-316 heavy chain | protein | 219 | 10% helix, 51% strand | — |
| L | Covox-316 light chain | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, H, L
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains E, L
- GOL · Glycerol · additive · 2 copies · chains E, H, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains H, L
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 | 864 | 0.71 | 0.76 | 84 | GOL, TRS |
| 2 | 139 | 0.43 | 0.75 | 25 | empty |
| 3 | 109 | 0.42 | 0.77 | 21 | empty |
| 4 | 96 | 0.40 | 0.77 | 22 | empty |
| 5 | 53 | 0.26 | 0.74 | 13 | FUC |
Interfaces
3 interfaces between chains.
- H–L · 1687 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 656 Ų buried · 10 hydrogen bonds · protein-protein
- E–L · 189 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7BEH · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in… · the same entry in another collection · chain E against E, 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 7BEH · PDBe 7BEH · UniProt P0DTC2
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