MolNFT v1 · #188375 · protein
Delta (B.1.617.2) SARS-cov-2 variant spike protein (S-gsas-delta) in the 3-rbd-down conformation; subclassification D6 state
7TOY · Spike glycoprotein: “Delta (B.1.617.2) SARS-cov-2 variant spike protein (S-gsas-delta) in the 3-rbd-down conformation…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #188375 on GenesisL1: 3D…
- PDB
- 7TOY
- Type
- protein
- Length
- 3,049 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 · 3 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1013 | 23% helix, 32% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1014 | 23% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1022 | 24% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 61 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 | 992 | 0.87 | 0.88 | 120 | empty |
| 2 | 897 | 0.84 | 0.86 | 108 | empty |
| 3 | 733 | 0.82 | 0.85 | 79 | empty |
| 4 | 987 | 0.81 | 0.83 | 99 | empty |
| 5 | 1154 | 0.81 | 0.82 | 101 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5424 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 5085 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 4704 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7TOY · Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down… · 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 7TOY · PDBe 7TOY · UniProt P0DTC2
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