Research workbench
Cryo-EM structure of SARS-cov-2 omicron spike protein with human ACE2 receptor, C2 state
Analyse Cryo-EM structure of SARS-cov-2 omicron spike protein with human ACE2 receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WVP
- Type
- protein
- Length
- 3,750 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
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 22% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 38% helix, 1% strand | Q9BYF1 |
| B, D | Spike glycoprotein | protein | 1048 | 17% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1057 | 18% helix, 30% strand | P0DTC2 |
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 | 1200 | 0.86 | 0.87 | 140 | empty |
| 2 | 633 | 0.83 | 0.88 | 95 | empty |
| 3 | 1195 | 0.83 | 0.84 | 111 | empty |
| 4 | 954 | 0.82 | 0.83 | 116 | empty |
| 5 | 464 | 0.80 | 0.87 | 38 | empty |
Interfaces
4 interfaces between chains.
- C–D · 4740 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4378 Ų buried · 37 hydrogen bonds · protein-protein
- B–D · 4228 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2408 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 7WVP · Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C2 state · 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 0.96
- 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 0.96
- 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 0.96
- 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 0.96
- 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 0.96
- 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 0.96
- 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 0.96
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 7WVP · PDBe 7WVP · UniProt Q9BYF1 · UniProt P0DTC2
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