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Crystal structure of the N501Y mutant receptor binding domain of SARS- cov-2 spike glycoprotein in complex with covox-269 Fab
Analyse Crystal structure of the N501Y mutant receptor binding domain of SARS- cov-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NEG
- Type
- protein
- Length
- 614 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody covox-269 Fab heavy chain; Antibody covox-269 Fab light chain; Surface…
- UniProt
- A0A7D5QNT3
- Ligands
- NAG, FUC, SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Antibody covox-269 Fab heavy chain | protein | 217 | 8% helix, 54% strand | — |
| L | Antibody covox-269 Fab light chain | protein | 214 | 5% helix, 51% strand | — |
| E | Surface glycoprotein | protein | 183 | 17% helix, 28% strand | A0A7D5QNT3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E
- FUC · alpha-L-fucopyranose · sugar
- SO4 · Sulfate ion · ion · 3 copies · chains H, E, L
- GOL · Glycerol · additive · 5 copies · chains H, L, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.61 | 0.80 | 38 | empty |
| 2 | 113 | 0.51 | 0.81 | 25 | GOL |
| 3 | 263 | 0.50 | 0.74 | 32 | empty |
| 4 | 72 | 0.43 | 0.80 | 18 | empty |
| 5 | 115 | 0.39 | 0.75 | 23 | GOL |
Interfaces
3 interfaces between chains.
- H–L · 1945 Ų buried · 19 hydrogen bonds · protein-protein
- H–E · 842 Ų buried · 22 hydrogen bonds · protein-protein
- L–E · 350 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7NEG · Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike… · 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 A0A7D5QNT3
- Elsewhere: RCSB PDB 7NEG · PDBe 7NEG · UniProt A0A7D5QNT3
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