Research workbench
Crystal structure of SARS-cov-2 rbd binding to dog ACE2
Analyse Crystal structure of SARS-cov-2 rbd binding to dog ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E3J
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACE2; Spike protein S1
- UniProt
- P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACE2 | protein | 695 | 58% helix, 8% strand | — |
| B | Spike protein S1 | protein | 195 | 15% helix, 27% strand | P0DTC2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.69 | 0.80 | 58 | empty |
| 2 | 563 | 0.68 | 0.78 | 62 | empty |
| 3 | 397 | 0.67 | 0.80 | 44 | empty |
| 4 | 87 | 0.49 | 0.82 | 16 | empty |
| 5 | 140 | 0.44 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 984 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E3J · Crystal structure of SARS-CoV-2 RBD binding to dog ACE2 · the same entry in another collection · chain B against B, 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 P0DTC2
- Elsewhere: RCSB PDB 7E3J · PDBe 7E3J · UniProt P0DTC2
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