MolNFT v1 · #186050 · protein
SARS-cov-2 S omicron spike B.1.1.529 - rbd down - 1-P2G3 Fab (local)
7QTK · Surface glycoprotein: “SARS-cov-2 S omicron spike B.1.1.529 - rbd down - 1-P2G3 Fab (local)”. Electron microscopy, 1 ligand (NAG), 6 pockets (best druggability 0.61). MolNFT v1 #186050 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7QTK
- Type
- protein
- Length
- 643 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface glycoprotein; P2G3 heavy chain; P2G3 light chain
- UniProt
- A0A8A4XEV3
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.61
Structure
electron microscopy · 3 distinct chains · 9% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Surface glycoprotein | protein | 201 | 12% helix, 22% strand | A0A8A4XEV3 |
| B | P2G3 heavy chain | protein | 228 | 8% helix, 46% strand | — |
| C | P2G3 light chain | protein | 214 | 7% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.61 | 0.86 | 27 | empty |
| 2 | 445 | 0.57 | 0.74 | 61 | empty |
| 3 | 181 | 0.50 | 0.77 | 26 | empty |
| 4 | 132 | 0.48 | 0.78 | 23 | empty |
| 5 | 69 | 0.31 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2109 Ų buried · 7 hydrogen bonds · protein-protein
- D–B · 601 Ų buried · 4 hydrogen bonds · protein-protein
- D–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7QTK · SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD down - 1-P2G3 Fab (Local) · the same entry in another collection · chain D against D, 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 A0A8A4XEV3
- Elsewhere: RCSB PDB 7QTK · PDBe 7QTK · UniProt A0A8A4XEV3
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