MolNFT v1 · #183625 · protein
Crystal structure of the receptor binding domain of SARS-cov-2 P.1 variant spike glycoprotein in complex with ACE2
7NXC · Processed angiotensin-converting enzyme 2: “Crystal structure of the receptor binding domain of SARS-cov-2 P.1 variant spike glycoprotein in complex with…”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.72).…
- PDB
- 7NXC
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike protein S1
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 596 | 63% helix, 4% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 195 | 14% helix, 27% 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.72 | 0.96 | 20 | empty |
| 2 | 947 | 0.71 | 0.75 | 74 | empty |
| 3 | 554 | 0.69 | 0.79 | 47 | empty |
| 4 | 298 | 0.56 | 0.76 | 49 | empty |
| 5 | 83 | 0.39 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7NXC · Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike… · the same entry in another collection · chain B against B, TM-score 1.00
- 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 1.00
- 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 1.00
- 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 0.99
- 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 0.99
- 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 0.99
- 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 0.99
- 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 0.98
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 P0DTC2
- Elsewhere: RCSB PDB 7NXC · PDBe 7NXC · UniProt Q9BYF1 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.