Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-47 Fab
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
- 7PS5
- Type
- protein
- Length
- 632 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-47 Fab heavy chain; Beta-47 Fab light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Beta-47 Fab heavy chain | protein | 224 | 8% helix, 50% strand | — |
| L | Beta-47 Fab light chain | protein | 215 | 5% helix, 48% strand | — |
| E | Spike protein S1 | protein | 193 | 11% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, E
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.59 | 0.75 | 52 | empty |
| 2 | 308 | 0.57 | 0.76 | 34 | empty |
| 3 | 263 | 0.53 | 0.75 | 37 | empty |
| 4 | 53 | 0.49 | 0.87 | 22 | empty |
| 5 | 70 | 0.39 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1899 Ų buried · 15 hydrogen bonds · protein-protein
- H–E · 648 Ų buried · 8 hydrogen bonds · protein-protein
- L–E · 263 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7PS5 · 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 7PS5 · PDBe 7PS5 · UniProt P0DTC2
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