Research workbench
SARS-cov-2 omicron BA.3 variant spike
Analyse SARS-cov-2 omicron BA.3 variant spike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XIY
- Type
- protein
- Length
- 3,255 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 19% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Spike glycoprotein | protein | 1085 | 19% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 47 copies · chains B, A, C
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 | 621 | 0.86 | 0.91 | 85 | empty |
| 2 | 947 | 0.85 | 0.87 | 114 | empty |
| 3 | 1094 | 0.83 | 0.84 | 115 | empty |
| 4 | 571 | 0.83 | 0.88 | 72 | empty |
| 5 | 502 | 0.83 | 0.89 | 72 | empty |
Interfaces
3 interfaces between chains.
- A–C · 6268 Ų buried · 52 hydrogen bonds · protein-protein
- B–A · 6096 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 6016 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 glycan, 33 disulfide (N-glycosylation, disulfide).
Compared structures
- 7XIY · SARS-CoV-2 Omicron BA.3 variant spike · the same entry in another collection · chain B against B, TM-score 1.00
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
- Elsewhere: RCSB PDB 7XIY · PDBe 7XIY · UniProt P0DTC2
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