MolNFT v1 · #176763 · protein
S protein of SARS-cov-2 in the locked conformation
7DWY · Spike glycoprotein: “S protein of SARS-cov-2 in the locked conformation”. Electron microscopy, 2 ligands (EIC, NAG), 20 pockets (best druggability 0.87). MolNFT v1 #176763 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7DWY
- Type
- protein
- Length
- 3,297 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- EIC, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1099 | 20% helix, 34% strand | P0DTC2 |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 3 copies · chains A, C, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 81 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 | 926 | 0.87 | 0.88 | 127 | empty |
| 2 | 1099 | 0.85 | 0.86 | 136 | empty |
| 3 | 320 | 0.84 | 0.93 | 44 | EIC |
| 4 | 272 | 0.84 | 0.94 | 34 | EIC |
| 5 | 1082 | 0.83 | 0.84 | 130 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6563 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 6511 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 6475 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7DWY · S protein of SARS-CoV-2 in the locked conformation · 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 7DWY · PDBe 7DWY · UniProt P0DTC2
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