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Crystal structure of the receptor binding domain of SARS-cov-2 P.1 variant spike glycoprotein in complex with covox-222 and EY6A fabs
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 P.1 variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NXB
- Type
- protein
- Length
- 1,050 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EY6A Fab heavy chain; EY6A Fab light chain; Spike protein S1; Covox-222 Fab heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, SO4
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | EY6A Fab heavy chain | protein | 214 | 4% helix, 48% strand | — |
| L | EY6A Fab light chain | protein | 213 | 3% helix, 52% strand | — |
| E | Spike protein S1 | protein | 193 | 17% helix, 30% strand | P0DTC2 |
| A | Covox-222 Fab heavy chain | protein | 217 | 7% helix, 51% strand | — |
| B | Covox-222 Fab light chain | protein | 213 | 8% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- SO4 · Sulfate ion · ion · 15 copies · chains H, E, A, B
- GOL · Glycerol · additive · 2 copies · chains E, A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.63 | 0.74 | 57 | PEG, SO4 |
| 2 | 184 | 0.62 | 0.83 | 29 | GOL |
| 3 | 306 | 0.58 | 0.77 | 46 | GOL |
| 4 | 271 | 0.53 | 0.75 | 36 | empty |
| 5 | 234 | 0.50 | 0.75 | 34 | SO4 |
Interfaces
6 interfaces between chains.
- H–L · 1925 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1669 Ų buried · 12 hydrogen bonds · protein-protein
- E–A · 684 Ų buried · 17 hydrogen bonds · protein-protein
- H–E · 644 Ų buried · 12 hydrogen bonds · protein-protein
- L–E · 439 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7NXB · Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant 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 P0DTC2
- Elsewhere: RCSB PDB 7NXB · PDBe 7NXB · UniProt P0DTC2
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