MolNFT v1 · #182515 · protein
Structure of SARS-cov-2 S2P spike at pH 7.4 refolded by low-pH treatment
7MTE · Spike glycoprotein: “Structure of SARS-cov-2 S2P spike at pH 7.4 refolded by low-pH treatment”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #182515 on GenesisL1: 3D structure, binding sites…
- PDB
- 7MTE
- Type
- protein
- Length
- 2,568 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 0.82
Structure
electron microscopy · 3 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 895 | 23% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 802 | 25% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 871 | 23% helix, 29% 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.82 | 0.85 | 52 | empty |
| 2 | 621 | 0.81 | 0.86 | 67 | empty |
| 3 | 910 | 0.80 | 0.82 | 72 | empty |
| 4 | 623 | 0.79 | 0.84 | 76 | empty |
| 5 | 949 | 0.77 | 0.80 | 80 | empty |
Interfaces
3 interfaces between chains.
- A–C · 4363 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 4256 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4004 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7MTE · Structure of SARS-CoV-2 S2P spike at pH 7.4 refolded by low-pH treatment · 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 7MTE · PDBe 7MTE · UniProt P0DTC2
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