Research workbench
SARS-cov-2 omicron variant rbd complexed with ACE2
Analyse SARS-cov-2 omicron variant rbd 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
- 7WPB
- Type
- protein
- Length
- 793 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
- Ligands
- NAG, ZN, CL
- Pockets
- 3 · best druggability 0.72
Structure
electron microscopy · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 198 | 12% helix, 27% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 595 | 60% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.72 | 0.76 | 102 | empty |
| 2 | 498 | 0.67 | 0.78 | 42 | empty |
| 3 | 310 | 0.58 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–D · 910 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7WPB · SARS-CoV-2 Omicron Variant RBD complexed with ACE2 · the same entry in another collection · chain D against D, TM-score 1.00
- 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 1.00
- 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 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 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 1.00
- 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 0.99
- 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 0.99
- 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 0.96
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 P0DTC2
- Every structure of UniProt Q9BYF1
- Elsewhere: RCSB PDB 7WPB · PDBe 7WPB · UniProt P0DTC2 · UniProt Q9BYF1
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