Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-50 and beta-54
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
- 7Q0H
- Type
- protein
- Length
- 1,067 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-54 Fab heavy chain; Beta-54 Fab light chain; Beta-50 Fab light chain; Beta-50 Fab…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Beta-54 Fab heavy chain | protein | 229 | 8% helix, 50% strand | — |
| L | Beta-54 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| B | Beta-50 Fab light chain | protein | 216 | 6% helix, 50% strand | — |
| A | Beta-50 Fab heavy chain | protein | 212 | 6% helix, 50% strand | — |
| E | Spike protein S1 | protein | 196 | 15% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, A, E
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.66 | 0.74 | 61 | empty |
| 2 | 660 | 0.65 | 0.75 | 73 | NAG, FUC |
| 3 | 274 | 0.59 | 0.78 | 39 | empty |
| 4 | 370 | 0.56 | 0.74 | 42 | empty |
| 5 | 209 | 0.51 | 0.76 | 26 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1939 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 1785 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 635 Ų buried · 7 hydrogen bonds · protein-protein
- H–E · 577 Ų buried · 8 hydrogen bonds · protein-protein
- H–B · 301 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q0H · Crystal structure of the receptor binding domain of SARS-CoV-2 beta 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 7Q0H · PDBe 7Q0H · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.