Research workbench
Crystal structure of spike protein receptor binding domain of escape mutant SARS-cov-2 from immunocompromised patient (D146*) in complex with human receptor ACE2
Analyse Crystal structure of spike protein receptor binding domain of escape mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SN0
- Type
- protein
- Length
- 1,582 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Surface glycoprotein
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, A0A7U0MIF7
- Ligands
- NAG, MAN, BMA, GAL, ZN, CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 62% helix, 5% strand | Q9BYF1 |
| C, D | Surface glycoprotein | protein | 194 | 14% helix, 28% strand | A0A7U0MIF7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains A, B, C, D
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains B, C, D
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains C
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 773 | 0.76 | 0.81 | 82 | empty |
| 2 | 517 | 0.70 | 0.80 | 61 | empty |
| 3 | 398 | 0.67 | 0.80 | 47 | empty |
| 4 | 484 | 0.67 | 0.78 | 48 | empty |
| 5 | 192 | 0.57 | 0.80 | 23 | NAG |
Interfaces
4 interfaces between chains.
- B–D · 962 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 307 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 300 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 7SN0 · Crystal structure of spike protein receptor binding domain of escape mutant SARS-CoV-2… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 1.00
- 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 1.00
- 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
- 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
- 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
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
- Every structure of UniProt A0A7U0MIF7
- Elsewhere: RCSB PDB 7SN0 · PDBe 7SN0 · UniProt Q9BYF1 · UniProt A0A7U0MIF7
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