MolNFT v1 · #181492 · protein
Mink cluster 5-associated SARS-cov-2 spike protein (S-gsas-D614G- delfv) in the 3-rbd down conformation
7LWJ · Spike glycoprotein: “Mink cluster 5-associated SARS-cov-2 spike protein (S-gsas-D614G- delfv) in the 3-rbd down conformation”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #181492 on GenesisL1…
- PDB
- 7LWJ
- Type
- protein
- Length
- 3,003 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 0.85
Structure
electron microscopy · 1 distinct chain · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1001 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 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 | 864 | 0.85 | 0.87 | 90 | empty |
| 2 | 564 | 0.84 | 0.90 | 69 | empty |
| 3 | 921 | 0.81 | 0.83 | 105 | empty |
| 4 | 854 | 0.80 | 0.83 | 82 | empty |
| 5 | 1155 | 0.76 | 0.78 | 82 | empty |
Interfaces
3 interfaces between chains.
- B–C · 4951 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 4815 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 4678 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7LWJ · Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down… · 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 7LWJ · PDBe 7LWJ · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.