MolNFT v1 · #178327 · protein
Structure of the SARS-cov-2 A372T spike glycoprotein (closed)
7FCE: “Structure of the SARS-cov-2 A372T spike glycoprotein (closed)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #178327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7FCE
- Type
- protein
- Length
- 3,125 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 · 2 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1043 | 22% helix, 31% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1041 | 22% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 78 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 | 1185 | 0.87 | 0.88 | 148 | empty |
| 2 | 1072 | 0.85 | 0.87 | 109 | empty |
| 3 | 771 | 0.85 | 0.89 | 99 | empty |
| 4 | 285 | 0.85 | 0.95 | 36 | empty |
| 5 | 714 | 0.85 | 0.88 | 70 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6334 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 6321 Ų buried · 45 hydrogen bonds · protein-protein
- B–C · 6315 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7FCE · Structure of the SARS-CoV-2 A372T spike glycoprotein (closed) · the same entry in another collection · chain C against C, 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 7FCE · PDBe 7FCE · UniProt P0DTC2
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