Research workbench
SARS-cov-2 omicron BA.2 variant rbd complexed with mouse ACE2
Analyse SARS-cov-2 omicron BA.2 variant rbd complexed with mouse ACE2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XOC
- Type
- protein
- Length
- 786 residues
- Chains
- 2
- 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
- Q8R0I0, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 5 · best druggability 0.69
Structure
electron microscopy · 2 distinct chains · 46% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 592 | 60% helix, 3% strand | Q8R0I0 |
| A | Spike glycoprotein | protein | 194 | 4% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D, A
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.69 | 0.76 | 73 | ZN |
| 2 | 440 | 0.65 | 0.78 | 47 | empty |
| 3 | 335 | 0.62 | 0.79 | 39 | empty |
| 4 | 85 | 0.32 | 0.73 | 19 | empty |
| 5 | 51 | 0.25 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- D–A · 841 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7XOC · SARS-CoV-2 Omicron BA.2 Variant RBD complexed with mouse ACE2 · the same entry in another collection · chain D against D, TM-score 1.00
- Q8R0I0 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q8R0I0) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 Q8R0I0
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7XOC · PDBe 7XOC · UniProt Q8R0I0 · UniProt P0DTC2
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