Research workbench
SARS-cov-2 omicron BA.1 variant rbd with mouse ACE2 bound
Analyse SARS-cov-2 omicron BA.1 variant rbd with mouse ACE2 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XO6
- 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 0.67
Structure
electron microscopy · 2 distinct chains · 49% 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 | 61% helix, 4% strand | Q8R0I0 |
| A | Spike glycoprotein | protein | 194 | 11% helix, 26% 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 | 514 | 0.67 | 0.78 | 56 | empty |
| 2 | 321 | 0.66 | 0.81 | 35 | empty |
| 3 | 284 | 0.65 | 0.82 | 28 | empty |
| 4 | 74 | 0.30 | 0.74 | 17 | empty |
| 5 | 51 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- D–A · 794 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 7XO6 · SARS-CoV-2 Omicron BA.1 Variant RBD with mouse ACE2 Bound · 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 0.93
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 7XO6 · PDBe 7XO6 · UniProt Q8R0I0 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.