MolNFT v1 · #179242 · protein
SARS-cov-2 spike in complex with LCB3 (local refinement of the rbd and LCB3)
7JZM: “SARS-cov-2 spike in complex with LCB3 (local refinement of the rbd and LCB3)”. Electron microscopy, 2 ligands (NAG, FUC), 3 pockets (best druggability 0.37). MolNFT v1 #179242 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7JZM
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LCB3; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 3 · best druggability 0.37
Structure
electron microscopy · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LCB3 | protein | 64 | 83% helix, 0% strand | — |
| B | Spike glycoprotein | protein | 194 | 15% helix, 30% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- FUC · alpha-L-fucopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.37 | 0.78 | 14 | empty |
| 2 | 83 | 0.34 | 0.75 | 17 | empty |
| 3 | 66 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JZM · SARS-CoV-2 spike in complex with LCB3 (local refinement of the RBD and LCB3) · 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 7JZM · PDBe 7JZM · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.