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Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-44 and beta-54 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
- 7PS6
- Type
- protein
- Length
- 1,060 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; Spike protein S1; Beta-44 Fab heavy…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, CL
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Beta-54 Fab heavy chain | protein | 229 | 9% helix, 49% strand | — |
| L | Beta-54 Fab light chain | protein | 214 | 6% helix, 51% strand | — |
| E | Spike protein S1 | protein | 182 | 17% helix, 26% strand | P0DTC2 |
| C | Beta-44 Fab heavy chain | protein | 221 | 10% helix, 50% strand | — |
| D | Beta-44 Fab light chain | protein | 214 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
- FUC · alpha-L-fucopyranose · sugar
- CL · Chloride ion · ion · chains C, D
- GOL · Glycerol · additive · 2 copies · chains E, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 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 | 711 | 0.64 | 0.74 | 62 | empty |
| 2 | 263 | 0.60 | 0.79 | 39 | empty |
| 3 | 441 | 0.60 | 0.75 | 51 | empty |
| 4 | 181 | 0.45 | 0.74 | 21 | CL |
| 5 | 92 | 0.40 | 0.77 | 25 | empty |
Interfaces
7 interfaces between chains.
- H–L · 1933 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1826 Ų buried · 13 hydrogen bonds · protein-protein
- H–E · 573 Ų buried · 10 hydrogen bonds · protein-protein
- E–C · 511 Ų buried · 3 hydrogen bonds · protein-protein
- E–D · 205 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7PS6 · 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 7PS6 · PDBe 7PS6 · UniProt P0DTC2
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