MolNFT v2 · #200336 · protein
SARS-CoV-2 Omicron BA.1 Variant Spike Trimer with one mouse ACE2 Bound
7XO5 · Spike glycoprotein: “SARS-CoV-2 Omicron BA.1 Variant Spike Trimer with one mouse ACE2 Bound”. Electron microscopy at 3.13, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.87). MolNFT v2 #200336 on GenesisL1: 3D structure…
- PDB
- 7XO5
- Type
- protein
- Length
- 3,659 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.13
- Source
- Mus musculus; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q8R0I0
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 3.13 · 3 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1024 | 20% helix, 28% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1022 | 20% helix, 29% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 591 | 48% helix, 2% strand | Q8R0I0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 37 copies · chains A, C, B, D
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.87 | 0.90 | 78 | empty |
| 2 | 915 | 0.85 | 0.87 | 123 | empty |
| 3 | 243 | 0.83 | 0.95 | 29 | empty |
| 4 | 977 | 0.82 | 0.84 | 103 | empty |
| 5 | 472 | 0.78 | 0.86 | 54 | empty |
Interfaces
4 interfaces between chains.
- B–C · 5150 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4882 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 4362 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 836 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 glycan, 27 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 7XO5 · SARS-cov-2 omicron BA.1 variant spike trimer with one mouse ACE2 bound · the same entry in another collection · chain A against A, 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 0.92
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 Q8R0I0
- Elsewhere: RCSB PDB 7XO5 · PDBe 7XO5 · UniProt P0DTC2 · UniProt Q8R0I0
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