Research workbench
The state 2 complex structure of omicron spike with BN03 (2-up rbd, 4 nanobodies)
Analyse The state 2 complex structure of omicron spike with BN03 (2-up rbd, 4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WHI
- Type
- protein
- Length
- 3,578 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; BN03_NANO1; BN03_NANO2
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 18% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1042 | 21% helix, 27% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1025 | 20% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1043 | 19% helix, 27% strand | P0DTC2 |
| D | BN03_NANO1 | protein | 117 | 3% helix, 31% strand | — |
| E, F | BN03_NANO1 | protein | 116 | 3% helix, 22% strand | — |
| G | BN03_NANO2 | protein | 119 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, 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 | 712 | 0.84 | 0.87 | 88 | empty |
| 2 | 750 | 0.81 | 0.84 | 86 | empty |
| 3 | 491 | 0.80 | 0.87 | 56 | empty |
| 4 | 488 | 0.77 | 0.85 | 54 | empty |
| 5 | 264 | 0.76 | 0.89 | 32 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4883 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 4550 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4410 Ų buried · 41 hydrogen bonds · protein-protein
- A–F · 1112 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1023 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 36 glycan (disulfide, N-glycosylation).
Compared structures
- 7WHI · The state 2 complex structure of Omicron spike with Bn03 (2-up RBD, 4 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 7WHI · PDBe 7WHI · UniProt P0DTC2
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