MolNFT v1 · #107620 · protein
Structure of the ectodomain of LGR5 in complex with R-spondin-2 (FU1FU2)
4UFR · Leucine-rich repeat-containing G-protein coupled receptor 5: “Structure of the ectodomain of LGR5 in complex with R-spondin-2 (FU1FU2)”. X-ray diffraction, 2 ligands (NAG, CL), 13 pockets (best druggability 0.75). MolNFT v1 #107620…
- PDB
- 4UFR
- Type
- protein
- Length
- 1,121 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-2
- UniProt
- O75473, Q8BFU0
- Ligands
- NAG, CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 459 | 5% helix, 19% strand | O75473 |
| B, D | R-spondin-2 | protein | 102 | 0% helix, 46% strand | Q8BFU0 |
| C | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 458 | 5% helix, 19% strand | O75473 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, C
- CL · Chloride ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.75 | 0.78 | 93 | CL |
| 2 | 349 | 0.71 | 0.83 | 43 | empty |
| 3 | 480 | 0.70 | 0.80 | 47 | CL |
| 4 | 397 | 0.68 | 0.81 | 43 | empty |
| 5 | 490 | 0.67 | 0.78 | 57 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1140 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 461 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4UFR · Structure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2) · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.99
- Q8BFU0 · AlphaFold monomer V2.0 prediction for R-spondin-2 (Q8BFU0) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q8BFU0
- Elsewhere: RCSB PDB 4UFR · PDBe 4UFR · UniProt O75473 · UniProt Q8BFU0
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