Research workbench
One rbd-up 2 of pre-fusion SARS-cov-2 gamma variant spike protein
Analyse One rbd-up 2 of pre-fusion SARS-cov-2 gamma variant spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SBT
- Type
- protein
- Length
- 3,300 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, FUC
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1104 | 23% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1096 | 23% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1100 | 23% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 86 copies · chains A, B, C
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 3 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.85 | 0.86 | 113 | empty |
| 2 | 1167 | 0.85 | 0.86 | 120 | empty |
| 3 | 844 | 0.82 | 0.84 | 94 | empty |
| 4 | 373 | 0.80 | 0.89 | 43 | empty |
| 5 | 446 | 0.79 | 0.87 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5627 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 5393 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 4796 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SBT · One RBD-up 2 of pre-fusion SARS-CoV-2 Gamma variant spike protein · 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 7SBT · PDBe 7SBT · UniProt P0DTC2
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