Research workbench
Cryo-EM structure of SARS-cov-2 omicron rbd in complex with human ACE2 ectodomain (local refinement)
Analyse Cryo-EM structure of SARS-cov-2 omicron rbd in complex with human ACE2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XCI
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike glycoprotein
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 6 · best druggability 0.73
Structure
electron microscopy · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 596 | 61% helix, 3% strand | Q9BYF1 |
| B | Spike glycoprotein | protein | 195 | 12% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.73 | 0.76 | 107 | empty |
| 2 | 564 | 0.69 | 0.78 | 57 | ZN |
| 3 | 92 | 0.57 | 0.86 | 18 | empty |
| 4 | 86 | 0.37 | 0.76 | 14 | empty |
| 5 | 70 | 0.31 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7XCI · Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with human ACE2 ectodomain (local… · 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 0.97
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 7XCI · PDBe 7XCI · UniProt Q9BYF1 · UniProt P0DTC2
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