Research workbench
SARS-cov-2 omicron variant spike trimer complexed with ACE2
Analyse SARS-cov-2 omicron variant spike trimer complexed with ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WPA
- Type
- protein
- Length
- 3,774 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, ZN, CL
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 22% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1061 | 18% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1057 | 19% helix, 27% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 595 | 35% helix, 2% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 45 copies · chains A, B, C, D
- ZN · Zinc ion · metal · chains D
- CL · Chloride ion · ion · chains 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 | 913 | 0.86 | 0.88 | 118 | empty |
| 2 | 854 | 0.85 | 0.87 | 102 | empty |
| 3 | 590 | 0.84 | 0.89 | 63 | empty |
| 4 | 443 | 0.83 | 0.90 | 61 | empty |
| 5 | 344 | 0.82 | 0.91 | 52 | empty |
Interfaces
4 interfaces between chains.
- B–C · 5997 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 5798 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 5022 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 935 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 glycan, 23 disulfide (N-glycosylation, disulfide).
Compared structures
- 7WPA · SARS-CoV-2 Omicron Variant SPIKE trimer complexed with ACE2 · the same entry in another collection · chain B against B, 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 D against A, TM-score 0.92
- 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 0.92
- 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 0.92
- 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 0.92
- 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 0.92
- 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 0.92
- 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 0.90
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 7WPA · PDBe 7WPA · UniProt P0DTC2 · UniProt Q9BYF1
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