Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 omicron variant spike glycoprotein in complex with its receptor human ACE2
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 omicron variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WBP
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike protein S1
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 63% helix, 4% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 195 | 13% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.69 | 0.81 | 38 | empty |
| 2 | 289 | 0.68 | 0.83 | 38 | empty |
| 3 | 68 | 0.62 | 0.91 | 18 | empty |
| 4 | 231 | 0.62 | 0.81 | 36 | empty |
| 5 | 59 | 0.34 | 0.77 | 14 | NAG |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7WBP · Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike… · 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 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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7WBP · PDBe 7WBP · UniProt Q9BYF1 · UniProt P0DTC2
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