MolNFT v1 · #177098 · protein
Cryo-EM structure of the SARS-cov-2 wild-type S-trimer from a subunit vaccine candidate
7E7D · Spike GLYCOPROTEIN,COLLAGEN alpha-1(I) chain: “Cryo-EM structure of the SARS-cov-2 wild-type S-trimer from a subunit vaccine candidate”. Electron microscopy, 2 ligands (ELA, NAG), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 7E7D
- Type
- protein
- Length
- 3,240 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, NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike GLYCOPROTEIN,COLLAGEN alpha-1(I) chain | protein | 1080 | 24% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- ELA · 9-octadecenoic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 83 copies · chains B, A, 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 | 1069 | 0.86 | 0.87 | 159 | empty |
| 2 | 220 | 0.85 | 0.97 | 33 | ELA |
| 3 | 961 | 0.84 | 0.86 | 124 | empty |
| 4 | 849 | 0.84 | 0.87 | 99 | empty |
| 5 | 752 | 0.84 | 0.87 | 90 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6778 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 6764 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 6539 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7E7D · Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate · 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 7E7D · PDBe 7E7D · UniProt P0DTC2
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