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Cryo-EM structure of SARS-cov-2 S-kappa variant (B.1.617.1), one rbd- up conformation 1
Analyse Cryo-EM structure of SARS-cov-2 S-kappa variant (B.1.617.1), one rbd- up… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V7E
- Type
- protein
- Length
- 3,093 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1031 | 21% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 82 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.87 | 0.88 | 118 | empty |
| 2 | 1094 | 0.87 | 0.88 | 129 | empty |
| 3 | 1059 | 0.80 | 0.82 | 80 | empty |
| 4 | 872 | 0.77 | 0.80 | 72 | empty |
| 5 | 81 | 0.73 | 0.95 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4331 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4123 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 3880 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 37 disulfide (N-glycosylation, disulfide).
Compared structures
- 7V7E · Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), one RBD-up conformation 1 · 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 7V7E · PDBe 7V7E · UniProt P0DTC2
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