Research workbench
Omicron spike bitrimer with 6M6 antibody
Analyse Omicron spike bitrimer 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
- 7WJZ
- Type
- protein
- Length
- 8,886 residues
- Chains
- 18
- 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 0.86
Structure
electron microscopy · 3 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, I, J, K, L, M | Spike glycoprotein | protein | 1045 | 18% helix, 24% strand | P0DTC2 |
| A, D, E, F, G, H | 6M6 heavy chain | protein | 226 | 1% helix, 31% strand | — |
| C, N, O, P, Q, R | 6M6 light chain | protein | 210 | 1% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains B, J, I, K, L, M
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 | 962 | 0.86 | 0.87 | 118 | empty |
| 2 | 882 | 0.86 | 0.88 | 106 | empty |
| 3 | 626 | 0.85 | 0.90 | 72 | empty |
| 4 | 996 | 0.82 | 0.83 | 98 | empty |
| 5 | 323 | 0.81 | 0.91 | 42 | empty |
Interfaces
39 interfaces between chains.
- L–M · 4736 Ų buried · 50 hydrogen bonds · protein-protein
- K–L · 4736 Ų buried · 50 hydrogen bonds · protein-protein
- K–M · 4729 Ų buried · 50 hydrogen bonds · protein-protein
- B–J · 4727 Ų buried · 51 hydrogen bonds · protein-protein
- B–I · 4709 Ų buried · 50 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 102 disulfide, 49 glycan (disulfide, N-glycosylation).
Compared structures
- 7WJZ · Omicron Spike bitrimer with 6m6 antibody · 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 P0DTC2
- Elsewhere: RCSB PDB 7WJZ · PDBe 7WJZ · UniProt P0DTC2
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