MolNFT v1 · #172037 · protein
Structure of SARS-cov-2 spike protein trimer (single arg S1/S2 cleavage site) in closed state
6ZP0 · Spike glycoprotein: “Structure of SARS-cov-2 spike protein trimer (single arg S1/S2 cleavage site) in closed state”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #172037 on GenesisL1: 3D…
- PDB
- 6ZP0
- Type
- protein
- Length
- 3,090 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 · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1030 | 22% helix, 33% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 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 | 1085 | 0.87 | 0.88 | 119 | empty |
| 2 | 1183 | 0.83 | 0.84 | 133 | empty |
| 3 | 700 | 0.81 | 0.85 | 86 | empty |
| 4 | 1187 | 0.81 | 0.82 | 120 | empty |
| 5 | 1121 | 0.79 | 0.81 | 103 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5445 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 5444 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 5434 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZP0 · Structure of SARS-CoV-2 Spike Protein Trimer (single Arg S1/S2 cleavage site) in Closed… · 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 6ZP0 · PDBe 6ZP0 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.