Research workbench
Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor
Analyse Structure of SARS coronavirus spike receptor-binding domain complexed with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AJF
- Type
- protein
- Length
- 1,542 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme-related carboxypeptidase (ACE2); SARS-coronavirus spike…
- EC
- 3.4.17.-
- UniProt
- Q9BYF1, P59594
- Ligands
- NAG, BMA, ZN, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme-related carboxypeptidase (ACE2) (EC 3.4.17.-) | protein | 597 | 63% helix, 4% strand | Q9BYF1 |
| E, F | SARS-coronavirus spike protein | protein | 174 | 15% helix, 22% strand | P59594 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, E, F
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains E, F
- 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
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.79 | 0.81 | 107 | ZN |
| 2 | 497 | 0.69 | 0.80 | 58 | empty |
| 3 | 459 | 0.66 | 0.78 | 42 | empty |
| 4 | 169 | 0.63 | 0.84 | 26 | empty |
| 5 | 261 | 0.61 | 0.80 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–E · 900 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 891 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 98 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 2AJF · Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor · the same entry in another collection · chain B against B, 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
- 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 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 1.00
- 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 1.00
- 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 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 Q9BYF1
- Every structure of UniProt P59594
- Elsewhere: RCSB PDB 2AJF · PDBe 2AJF · UniProt Q9BYF1 · UniProt P59594
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