Research workbench
Structure of freshly purified SARS-cov-2 S2P spike at pH 7.4
Analyse Structure of freshly purified SARS-cov-2 S2P spike at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MTC
- Type
- protein
- Length
- 2,642 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 · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 914 | 23% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 830 | 24% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 898 | 22% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 42 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.87 | 0.88 | 132 | empty |
| 2 | 932 | 0.83 | 0.84 | 113 | empty |
| 3 | 731 | 0.80 | 0.84 | 49 | empty |
| 4 | 871 | 0.78 | 0.81 | 76 | empty |
| 5 | 1039 | 0.78 | 0.80 | 89 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4484 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4234 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 4097 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7MTC · Structure of freshly purified SARS-CoV-2 S2P spike at pH 7.4 · 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 7MTC · PDBe 7MTC · UniProt P0DTC2
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