MolNFT v1 · #181499 · protein
Mink cluster 5-associated SARS-cov-2 spike PROTEIN(S-gsas-D614G-delfv) missing the S1 subunit and SD2 subdomain of one protomer
7LWQ · Spike glycoprotein: “Mink cluster 5-associated SARS-cov-2 spike PROTEIN(S-gsas-D614G-delfv) missing the S1 subunit and SD2…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #181499 on GenesisL1…
- PDB
- 7LWQ
- Type
- protein
- Length
- 2,425 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 · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Spike glycoprotein | protein | 1001 | 23% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 423 | 46% helix, 21% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains B, A, 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 | 654 | 0.82 | 0.87 | 57 | empty |
| 2 | 1140 | 0.82 | 0.83 | 102 | empty |
| 3 | 499 | 0.80 | 0.87 | 75 | empty |
| 4 | 431 | 0.75 | 0.85 | 61 | empty |
| 5 | 371 | 0.74 | 0.85 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–C · 5274 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 4144 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 2929 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7LWQ · Mink Cluster 5-associated SARS-CoV-2 spike protein(S-GSAS-D614G-delFV) missing the S1… · 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 7LWQ · PDBe 7LWQ · UniProt P0DTC2
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