Research workbench
Crystal structures of LGR4 and its complex with R-SPONDIN1
Analyse Crystal structures of LGR4 and its complex with R-SPONDIN1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LI1
- Type
- protein
- Length
- 849 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat-containing G-protein coupled receptor 4
- UniProt
- B0BLW3
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Leucine-rich repeat-containing G-protein coupled receptor 4 | protein | 425 | 4% helix, 17% strand | B0BLW3 |
| A | Leucine-rich repeat-containing G-protein coupled receptor 4 | protein | 424 | 6% helix, 18% strand | B0BLW3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.55 | 0.75 | 41 | empty |
| 2 | 61 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 427 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4LI1 · Crystal Structures of Lgr4 and its complex with R-spondin1 · the same entry in another collection · chain B against B, TM-score 1.00
- B0BLW3 · AlphaFold monomer V2.0 prediction for leucine-rich repeat-containing G-protein coupled… · a predicted model of the same protein · chain B against A, TM-score 0.91
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 B0BLW3
- Elsewhere: RCSB PDB 4LI1 · PDBe 4LI1 · UniProt B0BLW3
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