MolNFT v1 · #178718 · protein
Structure of SARS-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)
7JJI · Spike glycoprotein: “Structure of SARS-cov-2 3Q-2P full-length prefusion spike trimer (C3 symmetry)”. Electron microscopy, 3 ligands (VCG, EIC, NAG), 20 pockets (best druggability 0.88). MolNFT v1 #178718 on GenesisL1: 3D structure…
- PDB
- 7JJI
- Type
- protein
- Length
- 3,327 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- VCG, EIC, NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1109 | 22% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- VCG · 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside · ligand · 3 copies · chains A, B, C
- EIC · Linoleic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 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 | 759 | 0.88 | 0.91 | 89 | empty |
| 2 | 1113 | 0.86 | 0.87 | 109 | empty |
| 3 | 252 | 0.85 | 0.96 | 35 | EIC |
| 4 | 249 | 0.84 | 0.95 | 33 | EIC |
| 5 | 244 | 0.83 | 0.95 | 33 | EIC |
Interfaces
3 interfaces between chains.
- A–B · 6721 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 6720 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 6718 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7JJI · Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry) · 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 7JJI · PDBe 7JJI · UniProt P0DTC2
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