Research workbench
Cryo-EM structure of SARS-cov-2 kappa (B.1.617.1) Q484I spike protein
Analyse Cryo-EM structure of SARS-cov-2 kappa (B.1.617.1) Q484I spike protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TF2
- Type
- protein
- Length
- 6,228 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Spike glycoprotein | protein | 1038 | 22% helix, 35% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 120 copies · chains A, B, C, D, E, F
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 | 795 | 0.86 | 0.89 | 88 | empty |
| 2 | 817 | 0.86 | 0.89 | 85 | empty |
| 3 | 575 | 0.84 | 0.89 | 76 | empty |
| 4 | 623 | 0.83 | 0.88 | 88 | empty |
| 5 | 820 | 0.80 | 0.83 | 74 | empty |
Interfaces
12 interfaces between chains.
- D–E · 4692 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 4659 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4540 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 4502 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4493 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 84 glycan, 83 disulfide (N-glycosylation, disulfide).
Compared structures
- 7TF2 · Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein · 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 7TF2 · PDBe 7TF2 · UniProt P0DTC2
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