Research workbench
Structure of the SARS-cov-2 A372T spike glycoprotein (open)
Analyse Structure of the SARS-cov-2 A372T spike glycoprotein (open) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FCD
- Type
- protein
- Length
- 3,055 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 · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1007 | 21% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1021 | 19% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1027 | 20% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 35 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 | 1012 | 0.87 | 0.88 | 124 | empty |
| 2 | 698 | 0.83 | 0.87 | 97 | empty |
| 3 | 642 | 0.82 | 0.87 | 53 | empty |
| 4 | 274 | 0.82 | 0.93 | 36 | empty |
| 5 | 1018 | 0.80 | 0.82 | 112 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5032 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4764 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 4299 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 35 glycan (disulfide, N-glycosylation).
Compared structures
- 7FCD · Structure of the SARS-CoV-2 A372T spike glycoprotein (open) · the same entry in another collection · chain B against B, 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 7FCD · PDBe 7FCD · UniProt P0DTC2
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