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Structure of the ectodomain of LGR5 in complex with R-spondin-1 (FU1FU2) in P6122 crystal form
Analyse Structure of the ectodomain of LGR5 in complex with R-spondin-1 (FU1FU2) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BST
- Type
- protein
- Length
- 1,122 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine-rich repeat-containing G-protein coupled receptor 5; R-spondin-1
- UniProt
- O75473, Q2MKA7
- Ligands
- NAG, BMA
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 457 | 8% helix, 19% strand | O75473 |
| B | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 458 | 7% helix, 18% strand | O75473 |
| C | R-spondin-1 | protein | 103 | 0% helix, 44% strand | Q2MKA7 |
| D | R-spondin-1 | protein | 104 | 0% helix, 39% strand | Q2MKA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.78 | 0.94 | 26 | empty |
| 2 | 910 | 0.76 | 0.79 | 77 | empty |
| 3 | 92 | 0.76 | 0.97 | 21 | empty |
| 4 | 665 | 0.75 | 0.81 | 60 | empty |
| 5 | 507 | 0.74 | 0.82 | 57 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1123 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 963 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 634 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 575 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 516 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4BST · Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P6122 crystal… · the same entry in another collection · chain D against D, TM-score 1.00
- O75473 · 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 0.98
- Q2MKA7 · AlphaFold monomer V2.0 prediction for R-spondin-1 (Q2MKA7) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 O75473
- Every structure of UniProt Q2MKA7
- Elsewhere: RCSB PDB 4BST · PDBe 4BST · UniProt O75473 · UniProt Q2MKA7
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