MolNFT v1 · #156332 · protein
Crystal structure of SARS-cov-2 spike receptor-binding domain bound with ACE2
6M0J · Angiotensin-converting enzyme 2: “Crystal structure of SARS-cov-2 spike receptor-binding domain bound with ACE2”. X-ray diffraction, 3 ligands (NAG, ZN, CL), 4 pockets (best druggability 0.70). MolNFT v1 #156332 on GenesisL1: 3D…
- PDB
- 6M0J
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN, CL
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 64% helix, 4% strand | Q9BYF1 |
| E | Spike protein S1 | protein | 194 | 18% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, E
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 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 | 587 | 0.70 | 0.79 | 73 | empty |
| 2 | 410 | 0.69 | 0.81 | 43 | empty |
| 3 | 198 | 0.59 | 0.81 | 28 | empty |
| 4 | 55 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–E · 884 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6M0J · Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 · the same entry in another collection · chain E against E, 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 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 1.00
- 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 0.97
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 P0DTC2
- Elsewhere: RCSB PDB 6M0J · PDBe 6M0J · UniProt Q9BYF1 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.