Research workbench
Closed state of pre-fusion SARS-cov-2 kappa variant spike protein
Analyse Closed state of pre-fusion SARS-cov-2 kappa 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
- 7SBP
- Type
- protein
- Length
- 3,330 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 0.86
Structure
electron microscopy · 1 distinct chain · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1110 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 copies · chains A, C, B
- MAN · alpha-D-mannopyranose · sugar · 27 copies · chains C, 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 | 1044 | 0.86 | 0.87 | 131 | empty |
| 2 | 536 | 0.83 | 0.89 | 53 | empty |
| 3 | 1091 | 0.83 | 0.84 | 117 | empty |
| 4 | 283 | 0.82 | 0.93 | 37 | empty |
| 5 | 276 | 0.81 | 0.93 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6570 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 6456 Ų buried · 63 hydrogen bonds · protein-protein
- B–C · 6342 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SBP · Closed state of pre-fusion SARS-CoV-2 Kappa 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 7SBP · PDBe 7SBP · UniProt P0DTC2
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