MolNFT v1 · #190156 · protein
Cryo-EM structure of SARS-cov-2 omicron spike protein with human ACE2 (focus refinement on rbd-1/ACE2)
7WK6 · Spike glycoprotein: “Cryo-EM structure of SARS-cov-2 omicron spike protein with human ACE2 (focus refinement on rbd-1/ACE2)”. Electron microscopy, 7 pockets (best druggability 0.72). MolNFT v1 #190156 on GenesisL1: 3D structure…
- PDB
- 7WK6
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- 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
- Pockets
- 7 · best druggability 0.72
Structure
electron microscopy · 2 distinct chains · 40% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike glycoprotein | protein | 194 | 7% helix, 22% strand | P0DTC2 |
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 51% helix, 3% strand | Q9BYF1 |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.72 | 0.99 | 16 | empty |
| 2 | 265 | 0.64 | 0.81 | 30 | empty |
| 3 | 189 | 0.62 | 0.83 | 25 | empty |
| 4 | 189 | 0.59 | 0.81 | 28 | empty |
| 5 | 187 | 0.56 | 0.80 | 38 | empty |
Interfaces
1 interface between chains.
- E–A · 971 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 7WK6 · Cryo-EM structure of SARS-CoV-2 Omicron spike protein with human ACE2 (focus refinement… · the same entry in another collection · chain A against A, 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 0.99
- 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 0.99
- 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 0.99
- 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 0.99
- 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 P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7WK6 · PDBe 7WK6 · UniProt P0DTC2 · UniProt Q9BYF1
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