Research workbench
SARS-cov-2 spike in complex with LCB1 (local refinement of the rbd and LCB1)
Analyse SARS-cov-2 spike in complex with LCB1 (local refinement of the rbd and LCB1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZU
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LCB1; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 1 · best druggability 0.32
Structure
electron microscopy · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LCB1 | protein | 55 | 78% helix, 0% strand | — |
| B | Spike glycoprotein | protein | 193 | 16% 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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.32 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1054 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7JZU · SARS-CoV-2 spike in complex with LCB1 (local refinement of the RBD and LCB1) · 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 7JZU · PDBe 7JZU · UniProt P0DTC2
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