Research workbench
SARS-cov-2 D614G 3 rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-D614G sub-classification)
Analyse SARS-cov-2 D614G 3 rbd down spike protein trimer without the P986-P987… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KE6
- Type
- protein
- Length
- 2,916 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 0.82
Structure
electron microscopy · 1 distinct chain · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 972 | 23% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.82 | 0.83 | 96 | empty |
| 2 | 933 | 0.82 | 0.83 | 101 | empty |
| 3 | 642 | 0.82 | 0.86 | 64 | empty |
| 4 | 438 | 0.80 | 0.88 | 58 | empty |
| 5 | 250 | 0.79 | 0.92 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5540 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 5383 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 5203 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KE6 · SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer without the P986-P987 stabilizing… · 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 7KE6 · PDBe 7KE6 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.