MolNFT v1 · #188760 · protein
SARS-cov-2 omicron-BA.2 3-rbd down spike protein trimer without the P986-P987 stabilizing mutations (S-gsas-omicron-BA.2)
7UB5 · 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 0.87). MolNFT v1 #188760 on GenesisL1: 3D…
- PDB
- 7UB5
- Type
- protein
- Length
- 3,104 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 · 3 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1052 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1044 | 22% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1008 | 22% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains A, C, B
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 | 969 | 0.87 | 0.88 | 131 | empty |
| 2 | 1179 | 0.83 | 0.84 | 124 | empty |
| 3 | 1138 | 0.82 | 0.83 | 109 | empty |
| 4 | 1177 | 0.82 | 0.83 | 124 | empty |
| 5 | 518 | 0.79 | 0.86 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 6244 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 6201 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 5627 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 37 glycan (disulfide, N-glycosylation).
Compared structures
- 7UB5 · 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 7UB5 · PDBe 7UB5 · UniProt P0DTC2
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