Research workbench
SARS-cov-2 S protein S:D614G mutant 1-up
Analyse SARS-cov-2 S protein S:D614G mutant 1-up in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QDH
- Type
- protein
- Length
- 3,219 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,FIBRITIN
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,FIBRITIN | protein | 1070 | 20% helix, 27% strand | P0DTC2 |
| B | Spike GLYCOPROTEIN,FIBRITIN | protein | 1073 | 20% helix, 27% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,FIBRITIN | protein | 1076 | 21% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 44 copies · chains A, B, C
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 | 984 | 0.82 | 0.83 | 116 | empty |
| 2 | 668 | 0.82 | 0.86 | 77 | empty |
| 3 | 649 | 0.82 | 0.86 | 71 | empty |
| 4 | 686 | 0.80 | 0.85 | 67 | empty |
| 5 | 1181 | 0.80 | 0.81 | 100 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5177 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 4879 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 4842 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 32 glycan (disulfide, N-glycosylation).
Compared structures
- 7QDH · SARS-CoV-2 S protein S:D614G mutant 1-up · 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 7QDH · PDBe 7QDH · UniProt P0DTC2
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