Research workbench
Omicron spike trimer with 6M6 antibody
Analyse Omicron spike trimer with 6M6 antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WJY
- Type
- protein
- Length
- 3,756 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 6M6 heavy chain; 6M6 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 15% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1030 | 18% helix, 24% strand | P0DTC2 |
| B | 6M6 heavy chain | protein | 125 | 2% helix, 40% strand | — |
| C | 6M6 light chain | protein | 107 | 3% helix, 36% strand | — |
| D | Spike glycoprotein | protein | 1025 | 16% helix, 24% strand | P0DTC2 |
| E | 6M6 heavy chain | protein | 226 | 1% helix, 31% strand | — |
| F | 6M6 light chain | protein | 210 | 1% helix, 33% strand | — |
| G | Spike glycoprotein | protein | 1033 | 19% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, D, G
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 | 1112 | 0.85 | 0.86 | 131 | empty |
| 2 | 605 | 0.84 | 0.89 | 63 | empty |
| 3 | 361 | 0.82 | 0.91 | 53 | empty |
| 4 | 820 | 0.82 | 0.85 | 83 | empty |
| 5 | 418 | 0.77 | 0.86 | 34 | empty |
Interfaces
11 interfaces between chains.
- D–G · 5282 Ų buried · 50 hydrogen bonds · protein-protein
- A–G · 4720 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 4612 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1866 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1189 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 7WJY · Omicron spike trimer with 6m6 antibody · the same entry in another collection · chain C against C, 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 7WJY · PDBe 7WJY · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.