Research workbench
Local refine of omicron spike bitrimer with 6M6 antibody
Analyse Local refine of 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
- 7WK0
- Type
- protein
- Length
- 1,264 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6M6 heavy chain; 6M6 light chain; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 2% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 6M6 heavy chain | protein | 226 | 1% helix, 32% strand | — |
| B, E | 6M6 light chain | protein | 210 | 3% helix, 37% strand | — |
| C, F | Spike protein S1 | protein | 196 | 2% helix, 24% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 853 | 0.78 | 0.81 | 72 | empty |
| 2 | 506 | 0.59 | 0.74 | 58 | empty |
| 3 | 62 | 0.59 | 0.91 | 25 | empty |
| 4 | 96 | 0.58 | 0.86 | 28 | empty |
| 5 | 443 | 0.57 | 0.74 | 57 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1798 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1746 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1166 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1149 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 619 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7WK0 · Local refine of Omicron spike bitrimer with 6m6 antibody · 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 7WK0 · PDBe 7WK0 · UniProt P0DTC2
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