MolNFT v1 · #188758 · protein
SARS-cov-2 omicron-BA.2 3-rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-omicron-BA.2)
7UB0 · Spike glycoprotein: “SARS-cov-2 omicron-BA.2 3-rbd down spike protein trimer without the P986-P987 stabilizing mutations…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.86). MolNFT v1 #188758 on GenesisL1: 3D…
- PDB
- 7UB0
- Type
- protein
- Length
- 3,109 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 0.86
Structure
electron microscopy · 3 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1042 | 24% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1028 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1039 | 23% helix, 31% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 50 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 | 896 | 0.86 | 0.88 | 114 | empty |
| 2 | 751 | 0.84 | 0.87 | 97 | empty |
| 3 | 1037 | 0.84 | 0.85 | 104 | empty |
| 4 | 553 | 0.84 | 0.90 | 72 | empty |
| 5 | 953 | 0.83 | 0.85 | 111 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6174 Ų buried · 46 hydrogen bonds · protein-protein
- A–C · 6015 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 5884 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7UB0 · SARS-CoV-2 Omicron-BA.2 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing… · 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 7UB0 · PDBe 7UB0 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.