MolNFT v1 · #184942 · protein
Receptor-binding domain (rbd) of the spike protein of the bat coronavirus RATG13 virus in complex with the extracellular domain of human angiotensin-converting enzyme 2 (ACE2) - crystal form 1
7P8I · Processed angiotensin-converting enzyme 2: “Receptor-binding domain (rbd) of the spike protein of the bat coronavirus RATG13 virus in complex with the…”. X-ray diffraction, 2 ligands (NAG, BMA), 12 pockets (best druggability 0.79).…
- PDB
- 7P8I
- Type
- protein
- Length
- 1,579 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike glycoprotein
- UniProt
- Q9BYF1, A0A6B9WHD3
- Ligands
- NAG, BMA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 597 | 63% helix, 4% strand | Q9BYF1 |
| B, D | Spike glycoprotein | protein | 193 | 9% helix, 24% strand | A0A6B9WHD3 |
| C | Processed angiotensin-converting enzyme 2 | protein | 596 | 62% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.79 | 0.95 | 23 | empty |
| 2 | 544 | 0.73 | 0.81 | 62 | empty |
| 3 | 472 | 0.72 | 0.82 | 63 | empty |
| 4 | 392 | 0.71 | 0.82 | 47 | empty |
| 5 | 672 | 0.70 | 0.78 | 83 | empty |
Interfaces
3 interfaces between chains.
- A–B · 815 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 730 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 11 glycan (disulfide, N-glycosylation).
Compared structures
- 7P8I · Receptor-binding domain (RBD) of the spike protein of the bat coronavirus RaTG13 virus in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain C 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 0.98
- 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 0.98
- 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 0.97
- 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 0.97
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 A0A6B9WHD3
- Elsewhere: RCSB PDB 7P8I · PDBe 7P8I · UniProt Q9BYF1 · UniProt A0A6B9WHD3
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