Research workbench
The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies)
Analyse The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WHK
- Type
- protein
- Length
- 3,697 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.01
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Bn03_nano2; Bn03_nano1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.01 · 6 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1040 | 20% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1027 | 20% helix, 27% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1043 | 20% helix, 27% strand | P0DTC2 |
| D, H | Bn03_nano2 | protein | 119 | 0% helix, 37% strand | — |
| E | Bn03_nano1 | protein | 117 | 3% helix, 33% strand | — |
| F, G | Bn03_nano1 | protein | 116 | 3% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, E, C, B
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 | 722 | 0.87 | 0.90 | 66 | empty |
| 2 | 861 | 0.83 | 0.85 | 95 | empty |
| 3 | 665 | 0.82 | 0.87 | 72 | empty |
| 4 | 785 | 0.80 | 0.84 | 85 | empty |
| 5 | 555 | 0.80 | 0.86 | 52 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4862 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4306 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 4299 Ų buried · 39 hydrogen bonds · protein-protein
- B–E · 1090 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 1026 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide, 28 glycan (disulfide, N-glycosylation).
Compared structures
- 7WHK · The state 3 complex structure of omicron spike with BN03 (2-up rbd, 5 nanobodies) · 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 7WHK · PDBe 7WHK · UniProt P0DTC2
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