Research workbench
The state 1 complex structure of Omicron spike with Bn03 (1-up RBD, 3 nanobodies)
Analyse The state 1 complex structure of Omicron spike with Bn03 (1-up RBD, 3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WHJ
- Type
- protein
- Length
- 3,499 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.27
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Bn03_nano1; Bn03_nano2
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.27 · 5 distinct chains · 18% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1058 | 19% helix, 22% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1047 | 20% helix, 25% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1039 | 20% helix, 29% strand | P0DTC2 |
| D, E | Bn03_nano1 | protein | 118 | 0% helix, 23% strand | — |
| F | Bn03_nano2 | protein | 119 | 7% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 40 copies · chains A, D, B, C, F
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 | 1096 | 0.82 | 0.83 | 105 | empty |
| 2 | 841 | 0.82 | 0.85 | 94 | empty |
| 3 | 888 | 0.82 | 0.84 | 99 | empty |
| 4 | 577 | 0.81 | 0.86 | 44 | empty |
| 5 | 456 | 0.80 | 0.88 | 45 | empty |
Interfaces
9 interfaces between chains.
- A–B · 5455 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 4907 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4395 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1098 Ų buried · 13 hydrogen bonds · protein-protein
- B–E · 1022 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7WHJ · The state 1 complex structure of omicron spike with BN03 (1-up rbd, 3 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 7WHJ · PDBe 7WHJ · UniProt P0DTC2
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