Research workbench
SARS-cov-2 S-ACE2 complex
Analyse SARS-cov-2 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
- 7DF4
- Type
- protein
- Length
- 3,798 residues
- Chains
- 4
- 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
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 60% helix, 4% strand | Q9BYF1 |
| C | Spike glycoprotein | protein | 1065 | 21% helix, 30% strand | P0DTC2 |
| B, D | Spike glycoprotein | protein | 1068 | 22% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains C, D, B
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 | 931 | 0.86 | 0.88 | 130 | empty |
| 2 | 580 | 0.83 | 0.88 | 77 | empty |
| 3 | 1107 | 0.81 | 0.82 | 106 | empty |
| 4 | 641 | 0.81 | 0.86 | 81 | empty |
| 5 | 343 | 0.81 | 0.91 | 56 | empty |
Interfaces
4 interfaces between chains.
- C–D · 6233 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 5901 Ų buried · 61 hydrogen bonds · protein-protein
- C–B · 5234 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 1044 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 glycan, 42 disulfide (N-glycosylation, disulfide, O-glycosylation, glycosylation).
Compared structures
- 7DF4 · SARS-CoV-2 S-ACE2 complex · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- 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 0.97
- 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 0.97
- 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 0.97
- 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 0.97
- 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 0.97
- 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 0.97
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 7DF4 · PDBe 7DF4 · UniProt Q9BYF1 · UniProt P0DTC2
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