MolNFT v1 · #189809 · protein
ACE2-rbd in SARS-cov-2 beta variant S-ACE2 complex
7VX4 · Angiotensin-converting enzyme 2: “ACE2-rbd in SARS-cov-2 beta variant S-ACE2 complex”. Electron microscopy, 2 ligands (NAG, ZN), 6 pockets (best druggability 0.71). MolNFT v1 #189809 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7VX4
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- electron microscopy
- 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, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 6 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 62% helix, 4% strand | Q9BYF1 |
| E | Spike glycoprotein | protein | 194 | 14% helix, 25% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.71 | 0.82 | 51 | empty |
| 2 | 122 | 0.65 | 0.88 | 21 | empty |
| 3 | 199 | 0.60 | 0.82 | 22 | empty |
| 4 | 103 | 0.40 | 0.76 | 16 | empty |
| 5 | 64 | 0.34 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–E · 1002 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7VX4 · ACE2-RBD in SARS-CoV-2 Beta variant S-ACE2 complex · 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 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 0.99
- 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 0.98
- 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
- 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 7VX4 · PDBe 7VX4 · UniProt Q9BYF1 · UniProt P0DTC2
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