Research workbench
Cryo-EM structure of triple ACE2-bound SARS-cov-2 trimer spike at pH 7.4
Analyse Cryo-EM structure of triple ACE2-bound SARS-cov-2 trimer spike at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KMS
- Type
- protein
- Length
- 4,887 residues
- Chains
- 6
- 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 0.82
Structure
electron microscopy · 3 distinct chains · 28% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, D, E | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 56% helix, 3% strand | Q9BYF1 |
| A, C | Spike glycoprotein | protein | 1033 | 20% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1033 | 21% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains F, A, C, B, D, E
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 | 694 | 0.82 | 0.86 | 82 | empty |
| 2 | 1049 | 0.81 | 0.82 | 133 | empty |
| 3 | 575 | 0.80 | 0.86 | 43 | empty |
| 4 | 304 | 0.79 | 0.91 | 45 | empty |
| 5 | 258 | 0.77 | 0.90 | 41 | empty |
Interfaces
6 interfaces between chains.
- C–B · 4436 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 4435 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4399 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 935 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 63 glycan, 48 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KMS · Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4 · 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 F against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F 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 F 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 7KMS · PDBe 7KMS · UniProt Q9BYF1 · UniProt P0DTC2
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