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Structure of SARS-cov-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (S19W,N330Y)
Analyse Structure of SARS-cov-2 spike receptor-binding domain in complex with high… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EFP
- Type
- protein
- Length
- 790 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike glycoprotein
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 596 | 63% helix, 4% strand | Q9BYF1 |
| B | Spike glycoprotein | protein | 194 | 16% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.85 | 0.89 | 75 | empty |
| 2 | 248 | 0.70 | 0.85 | 35 | empty |
| 3 | 199 | 0.69 | 0.86 | 27 | empty |
| 4 | 210 | 0.55 | 0.79 | 26 | empty |
| 5 | 77 | 0.32 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 983 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7EFP · Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2… · the same entry in another collection · 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 A against A, TM-score 0.95
- 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 0.88
- 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 0.88
- 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 0.88
- 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 0.88
- 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 0.88
- 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 0.88
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 P0DTC2
- Elsewhere: RCSB PDB 7EFP · PDBe 7EFP · UniProt Q9BYF1 · UniProt P0DTC2
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