Research workbench
Structural basis of SARS-cov-2-closely-related bat coronavirus RATG13 to HACE2
Analyse Structural basis of SARS-cov-2-closely-related bat coronavirus RATG13 to HACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DRV
- 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; Spike glycoprotein
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, A0A6B9WHD3
- Ligands
- NAG, ZN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 61% helix, 4% strand | Q9BYF1 |
| C, D | Spike glycoprotein | protein | 195 | 12% helix, 27% strand | A0A6B9WHD3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.82 | 0.83 | 106 | empty |
| 2 | 119 | 0.74 | 0.93 | 34 | empty |
| 3 | 377 | 0.72 | 0.83 | 43 | empty |
| 4 | 542 | 0.67 | 0.78 | 56 | empty |
| 5 | 383 | 0.67 | 0.81 | 46 | empty |
Interfaces
3 interfaces between chains.
- A–C · 853 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 813 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7DRV · Structural basis of SARS-CoV-2-closely-related bat coronavirus RaTG13 to hACE2 · 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 0.99
- 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 0.98
- 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 0.98
- 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 0.98
- 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 0.98
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 7DRV · PDBe 7DRV · UniProt Q9BYF1 · UniProt A0A6B9WHD3
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