MolNFT v1 · #187983 · protein
SARS-cov-2 S (spike glycoprotein) D614G with ONE(1) rbd up
7T67: “SARS-cov-2 S (spike glycoprotein) D614G with ONE(1) rbd up”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #187983 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7T67
- Type
- protein
- Length
- 3,075 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 0.88
Structure
electron microscopy · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Spike glycoprotein | protein | 1025 | 22% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, C, G
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 | 1152 | 0.88 | 0.89 | 126 | empty |
| 2 | 1179 | 0.86 | 0.86 | 123 | empty |
| 3 | 1117 | 0.82 | 0.83 | 101 | empty |
| 4 | 1071 | 0.80 | 0.81 | 88 | empty |
| 5 | 754 | 0.73 | 0.79 | 47 | empty |
Interfaces
3 interfaces between chains.
- C–G · 4446 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 4331 Ų buried · 37 hydrogen bonds · protein-protein
- A–G · 4245 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7T67 · SARS-CoV-2 S (Spike Glycoprotein) D614G with One(1) RBD 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 7T67 · PDBe 7T67 · UniProt P0DTC2
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