MolNFT v1 · #190574 · protein
SARS-cov-2 omicron BA.2 variant spike (state 1)
7XIW · Spike glycoprotein: “SARS-cov-2 omicron BA.2 variant spike (state 1)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #190574 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XIW
- Type
- protein
- Length
- 3,310 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 0.85
Structure
electron microscopy · 3 distinct chains · 19% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1103 | 20% helix, 26% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1102 | 19% helix, 26% strand | P0DTC2 |
| D | Spike glycoprotein | protein | 1105 | 19% helix, 21% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 56 copies · chains A, B, 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 | 864 | 0.85 | 0.87 | 97 | empty |
| 2 | 789 | 0.84 | 0.87 | 83 | empty |
| 3 | 1129 | 0.83 | 0.84 | 113 | empty |
| 4 | 1085 | 0.83 | 0.84 | 115 | empty |
| 5 | 616 | 0.82 | 0.87 | 61 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5781 Ų buried · 47 hydrogen bonds · protein-protein
- B–D · 5450 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 4354 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 glycan, 36 disulfide (N-glycosylation, disulfide).
Compared structures
- 7XIW · SARS-CoV-2 Omicron BA.2 variant spike (state 1) · the same entry in another collection · chain A against A, 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 7XIW · PDBe 7XIW · UniProt P0DTC2
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