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Crystal structure of chimeric omicron rbd (strain BA.1) complexed with human ACE2
Analyse Crystal structure of chimeric omicron rbd (strain BA.1) complexed with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U0N
- Type
- protein
- Length
- 1,570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23
- UniProt
- Q9BYF1
- Ligands
- NAG, BMA, ZN, MG, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 596 | 64% helix, 4% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 188 | 14% helix, 30% strand | — |
| F | Spike protein S1 | protein | 190 | 10% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains B, A, E, F
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains E, F
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- CL · Chloride ion · ion · 5 copies · chains A, B, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.79 | 0.84 | 60 | ZN |
| 2 | 1026 | 0.76 | 0.79 | 108 | empty |
| 3 | 550 | 0.67 | 0.77 | 62 | empty |
| 4 | 449 | 0.64 | 0.77 | 57 | empty |
| 5 | 134 | 0.58 | 0.84 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–F · 921 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 920 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 134 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 glycan, 13 disulfide (N-glycosylation, disulfide).
Compared structures
- 7U0N · Crystal structure of chimeric omicron RBD (strain BA.1) complexed with human ACE2 · the same entry in another collection · chain A against A, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9BYF1
- Elsewhere: RCSB PDB 7U0N · PDBe 7U0N · UniProt Q9BYF1
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