Research workbench
SARS-cov-2 B.1.1.7 S-ACE2 complex
Analyse SARS-cov-2 B.1.1.7 S-ACE2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FEM
- Type
- protein
- Length
- 3,579 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 997 | 21% helix, 25% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1001 | 21% helix, 27% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1003 | 21% helix, 28% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23) | protein | 578 | 52% helix, 2% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.88 | 0.89 | 104 | empty |
| 2 | 864 | 0.81 | 0.83 | 85 | empty |
| 3 | 177 | 0.80 | 0.95 | 31 | empty |
| 4 | 623 | 0.79 | 0.85 | 59 | empty |
| 5 | 889 | 0.79 | 0.81 | 85 | empty |
Interfaces
4 interfaces between chains.
- A–C · 4744 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 4701 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 4376 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 904 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 glycan, 41 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7FEM · SARS-CoV-2 B.1.1.7 S-ACE2 complex · 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 D against A, TM-score 0.95
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.95
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.93
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
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7FEM · PDBe 7FEM · UniProt P0DTC2 · UniProt Q9BYF1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.