Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 beta variant spike glycoprotein in complex with beta-40 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
- 7PS7
- Type
- protein
- Length
- 1,250 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Beta-40 Fab light chain; Beta-40 heavy chain
- UniProt
- P0DTC2
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, R | Spike protein S1 | protein | 194 | 15% helix, 30% strand | P0DTC2 |
| L, B | Beta-40 Fab light chain | protein | 210 | 7% helix, 49% strand | — |
| A, H | Beta-40 heavy chain | protein | 221 | 4% helix, 52% strand | — |
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 | 832 | 0.73 | 0.78 | 52 | empty |
| 2 | 400 | 0.65 | 0.79 | 49 | empty |
| 3 | 509 | 0.63 | 0.76 | 52 | empty |
| 4 | 508 | 0.63 | 0.76 | 56 | empty |
| 5 | 259 | 0.56 | 0.77 | 44 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1955 Ų buried · 15 hydrogen bonds · protein-protein
- B–A · 1949 Ų buried · 15 hydrogen bonds · protein-protein
- E–R · 864 Ų buried · 9 hydrogen bonds · protein-protein
- R–H · 459 Ų buried · 5 hydrogen bonds · protein-protein
- E–A · 454 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 7PS7 · Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike… · the same entry in another collection · chain E against E, 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 7PS7 · PDBe 7PS7 · UniProt P0DTC2
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