Research workbench
SARS-cov-2 S omicron spike B.1.1.529 - rbd up - 1-P2G3 and 1-P5C3 fabs (local)
Analyse SARS-cov-2 S omicron spike B.1.1.529 - rbd up - 1-P2G3 and 1-P5C3 fabs (local) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QTJ
- Type
- protein
- Length
- 1,280 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P2G3 heavy chain; P2G3 light chain; Surface glycoprotein; P5C3 light chain; P5C3 heavy…
- UniProt
- A0A8A4XEV3
- Ligands
- NAG, BMA
- Pockets
- 17 · best druggability 0.70
Structure
electron microscopy · 5 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | P2G3 heavy chain | protein | 228 | 7% helix, 44% strand | — |
| C | P2G3 light chain | protein | 214 | 6% helix, 46% strand | — |
| A, D | Surface glycoprotein | protein | 201 | 11% helix, 23% strand | A0A8A4XEV3 |
| E | P5C3 light chain | protein | 215 | 6% helix, 43% strand | — |
| F | P5C3 heavy chain | protein | 221 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.70 | 0.96 | 18 | empty |
| 2 | 78 | 0.67 | 0.93 | 20 | empty |
| 3 | 162 | 0.62 | 0.84 | 35 | empty |
| 4 | 123 | 0.61 | 0.86 | 27 | empty |
| 5 | 334 | 0.59 | 0.77 | 56 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2078 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1831 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 684 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 401 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 338 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7QTJ · SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD up - 1-P2G3 and 1-P5C3 Fabs (Local) · the same entry in another collection · chain B against B, 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 7QTJ · PDBe 7QTJ · UniProt A0A8A4XEV3
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