Research workbench
Cryo-EM structure of the SARS-cov-2 furin site mutant S-trimer from a subunit vaccine candidate
Analyse Cryo-EM structure of the SARS-cov-2 furin site mutant S-trimer from a subunit… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E7B
- Type
- protein
- Length
- 3,306 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,COLLAGEN alpha-1(I) chain
- UniProt
- P0DTC2
- Ligands
- ELA, VCG, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike GLYCOPROTEIN,COLLAGEN alpha-1(I) chain | protein | 1102 | 22% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- ELA · 9-octadecenoic acid · ligand · 3 copies · chains A, C, B
- 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, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 93 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 | 1117 | 0.86 | 0.87 | 123 | empty |
| 2 | 241 | 0.85 | 0.96 | 33 | ELA |
| 3 | 751 | 0.85 | 0.88 | 65 | empty |
| 4 | 238 | 0.84 | 0.96 | 33 | ELA |
| 5 | 238 | 0.84 | 0.95 | 33 | ELA |
Interfaces
3 interfaces between chains.
- A–B · 6634 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 6619 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 6617 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7E7B · Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine… · 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 7E7B · PDBe 7E7B · UniProt P0DTC2
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