MolNFT v1 · #190152 · protein
SARS-cov-2 omicron S-close
7WK2 · Spike glycoprotein: “SARS-cov-2 omicron S-close”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #190152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7WK2
- Type
- protein
- Length
- 3,171 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 19% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1057 | 19% helix, 28% strand | P0DTC2 |
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 | 683 | 0.89 | 0.93 | 89 | empty |
| 2 | 1029 | 0.86 | 0.87 | 118 | empty |
| 3 | 669 | 0.84 | 0.88 | 88 | empty |
| 4 | 392 | 0.80 | 0.88 | 39 | empty |
| 5 | 961 | 0.79 | 0.81 | 81 | empty |
Interfaces
3 interfaces between chains.
- A–B · 5524 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 5444 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 5366 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide (disulfide).
Compared structures
- 7WK2 · SARS-CoV-2 Omicron S-close · 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 7WK2 · PDBe 7WK2 · UniProt P0DTC2
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