MolNFT v1 · #173908 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in a ternary complex with covox-384 and S309 fabs
7BEP: “Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in a ternary complex with…”. X-ray diffraction, 7 ligands (GLY, GLU, NAG), 20 pockets (best druggability 0.77). MolNFT v1 #173908 on GenesisL1: 3D…
- PDB
- 7BEP
- Type
- protein
- Length
- 2,175 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-384 heavy chain; Covox-384 light chain; S309 heavy chain; S309…
- UniProt
- P0DTC2
- Ligands
- GLY, GLU, NAG, MAN, BMA, FUC, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, C | Spike glycoprotein | protein | 197 | 15% helix, 28% strand | P0DTC2 |
| A | Covox-384 heavy chain | protein | 228 | 7% helix, 49% strand | — |
| B, F | Covox-384 light chain | protein | 218 | 5% helix, 50% strand | — |
| H | S309 heavy chain | protein | 230 | 9% helix, 50% strand | — |
| L, I | S309 light chain | protein | 214 | 7% helix, 51% strand | — |
| D | Covox-384 heavy chain | protein | 227 | 7% helix, 49% strand | — |
| G | S309 heavy chain | protein | 232 | 10% helix, 50% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · 6 copies · chains A, H, G, L, D, F, I
- GLU · Glutamic acid · ligand · 2 copies · chains A, B, D, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, H, L, C, G, I
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains H, G
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H, L, G, I
- CL · Chloride ion · ion · 10 copies · chains A, B, H, L, C, D, F, G, I
- IMD · Imidazole · additive · 5 copies · chains E, H, L, C, G
- GOL · Glycerol · additive · 4 copies · chains E, H, D, F, C, G, I
- PG4 · Tetraethylene glycol · additive · 2 copies · chains H, L, G, I
- PGE · Triethylene glycol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.77 | 0.79 | 120 | PEG |
| 2 | 934 | 0.76 | 0.79 | 101 | empty |
| 3 | 710 | 0.68 | 0.76 | 84 | NAG, FUC, IMD |
| 4 | 269 | 0.66 | 0.82 | 43 | empty |
| 5 | 697 | 0.65 | 0.74 | 80 | GLY, PG4 |
Interfaces
20 interfaces between chains.
- D–F · 2061 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2034 Ų buried · 18 hydrogen bonds · protein-protein
- G–I · 1941 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1907 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 661 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7BEP · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a… · the same entry in another collection · chain C against C, 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 7BEP · PDBe 7BEP · UniProt P0DTC2
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