Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with covox-45 and beta-6 fabs
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 beta variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PRY
- Type
- protein
- Length
- 2,112 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Covox-45 Fab heavy chain; Covox-45 Fab light chain; Beta-6 Fab heavy chain; Beta-6 Fab…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.58
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Covox-45 Fab heavy chain | protein | 216 | 6% helix, 51% strand | — |
| B, G | Covox-45 Fab light chain | protein | 213 | 6% helix, 49% strand | — |
| H | Beta-6 Fab heavy chain | protein | 218 | 5% helix, 51% strand | — |
| L, D | Beta-6 Fab light chain | protein | 215 | 5% helix, 47% strand | — |
| E, I | Spike protein S1 | protein | 193 | 17% helix, 28% strand | P0DTC2 |
| C | Beta-6 Fab heavy chain | protein | 220 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, I
- FUC · alpha-L-fucopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.58 | 0.76 | 35 | empty |
| 2 | 278 | 0.58 | 0.78 | 36 | empty |
| 3 | 415 | 0.57 | 0.74 | 57 | empty |
| 4 | 136 | 0.55 | 0.82 | 23 | empty |
| 5 | 300 | 0.55 | 0.75 | 35 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2136 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 2071 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1621 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1617 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 836 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7PRY · Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike… · 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 P0DTC2
- Elsewhere: RCSB PDB 7PRY · PDBe 7PRY · UniProt P0DTC2
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