MolNFT v1 · #190562 · protein
S-ecd (omicron) in complex with STS165
7XIC · Spike glycoprotein: “S-ecd (omicron) in complex with STS165”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #190562 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XIC
- Type
- protein
- Length
- 3,706 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Heavy chain of STS165; Light chain of STS165
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 999 | 23% helix, 32% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 998 | 22% helix, 33% strand | P0DTC2 |
| E, H, K | Heavy chain of STS165 | protein | 129 | 5% helix, 48% strand | — |
| F, I, L | Light chain of STS165 | protein | 108 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains A, B, 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 | 913 | 0.88 | 0.90 | 110 | empty |
| 2 | 868 | 0.86 | 0.88 | 87 | empty |
| 3 | 1132 | 0.83 | 0.84 | 125 | empty |
| 4 | 788 | 0.77 | 0.81 | 80 | empty |
| 5 | 143 | 0.74 | 0.92 | 25 | empty |
Interfaces
12 interfaces between chains.
- A–C · 3972 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 3963 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 3768 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1048 Ų buried · 13 hydrogen bonds · protein-protein
- H–I · 1048 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7XIC · S-ECD (Omicron) in complex with STS165 · 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 7XIC · PDBe 7XIC · UniProt P0DTC2
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