Research workbench
The receptor binding domain of SARS-cov-2 spike glycoprotein in complex with covox-58 and covox-158 fabs
Analyse The receptor binding domain of SARS-cov-2 spike glycoprotein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QNY
- Type
- protein
- Length
- 1,046 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-58 heavy chain; Covox-58 light chain; Surface glycoprotein; Covox-158 heavy chain…
- UniProt
- A0A894R379
- Ligands
- NAG, NA
- Pockets
- 12 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Covox-58 heavy chain | protein | 224 | 3% helix, 53% strand | — |
| B | Covox-58 light chain | protein | 211 | 8% helix, 50% strand | — |
| E | Surface glycoprotein | protein | 183 | 14% helix, 27% strand | A0A894R379 |
| H | Covox-158 heavy chain | protein | 216 | 7% helix, 53% strand | — |
| L | Covox-158 light chain | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- NA · Sodium ion · metal · chains H, L
- GOL · Glycerol · additive · 2 copies · chains B, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.59 | 0.76 | 41 | NA |
| 2 | 448 | 0.57 | 0.74 | 51 | empty |
| 3 | 64 | 0.55 | 0.88 | 22 | empty |
| 4 | 299 | 0.53 | 0.75 | 43 | empty |
| 5 | 213 | 0.48 | 0.75 | 35 | empty |
Interfaces
6 interfaces between chains.
- H–L · 1773 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 1060 Ų buried · 14 hydrogen bonds · protein-protein
- E–H · 697 Ų buried · 18 hydrogen bonds · protein-protein
- E–L · 432 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7QNY · The receptor binding domain of SARS-CoV-2 spike glycoprotein in complex with COVOX-58 and… · the same entry in another collection · chain A against A, 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 A0A894R379
- Elsewhere: RCSB PDB 7QNY · PDBe 7QNY · UniProt A0A894R379
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