Research workbench
Cryo-EM structure of single ACE2-bound SARS-cov-2 trimer spike at pH 5.5
Analyse Cryo-EM structure of single ACE2-bound SARS-cov-2 trimer spike at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KNE
- Type
- protein
- Length
- 3,637 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, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Spike glycoprotein | protein | 1006 | 22% helix, 25% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1029 | 21% helix, 26% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 54% helix, 2% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 56 copies · chains C, A, B, D
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 | 1138 | 0.87 | 0.88 | 150 | empty |
| 2 | 894 | 0.83 | 0.85 | 108 | empty |
| 3 | 636 | 0.83 | 0.87 | 74 | empty |
| 4 | 828 | 0.82 | 0.84 | 83 | empty |
| 5 | 648 | 0.80 | 0.85 | 56 | empty |
Interfaces
4 interfaces between chains.
- C–A · 5038 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 4905 Ų buried · 39 hydrogen bonds · protein-protein
- C–B · 4457 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1071 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KNE · Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5 · 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 D against A, TM-score 0.96
- 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
- 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 0.94
- 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 0.94
- 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 0.94
- 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 0.94
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 7KNE · PDBe 7KNE · UniProt P0DTC2 · UniProt Q9BYF1
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