Research workbench
Crystal structure of SARS-cov-2 rbd binding to pangolin ACE2
Analyse Crystal structure of SARS-cov-2 rbd binding to pangolin ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DHX
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pangolin ACE2; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pangolin ACE2 | protein | 593 | 63% helix, 4% strand | — |
| B | Spike glycoprotein | protein | 195 | 15% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.70 | 0.75 | 71 | empty |
| 2 | 524 | 0.69 | 0.79 | 45 | empty |
| 3 | 386 | 0.66 | 0.79 | 32 | empty |
| 4 | 51 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7DHX · Crystal structure of SARS-CoV-2 RBD binding to pangolin ACE2 · the same entry in another collection · 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 P0DTC2
- Elsewhere: RCSB PDB 7DHX · PDBe 7DHX · UniProt P0DTC2
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