Research workbench
Structure of the ectodomain of LGR5 in complex with R-spondin-1 (FU1FU2) in P21 crystal form
Analyse Structure of the ectodomain of LGR5 in complex with R-spondin-1 (FU1FU2) in P21… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BSS
- Type
- protein
- Length
- 2,281 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 466 | 4% helix, 17% strand | O75473 |
| B | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 469 | 4% helix, 18% strand | O75473 |
| C, G | R-spondin-1 | protein | 103 | 0% helix, 44% strand | Q2MKA7 |
| D, H | R-spondin-1 | protein | 104 | 0% helix, 43% strand | Q2MKA7 |
| E | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 468 | 4% helix, 17% strand | O75473 |
| F | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 464 | 5% helix, 17% strand | O75473 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.80 | 0.82 | 92 | empty |
| 2 | 1173 | 0.80 | 0.81 | 114 | empty |
| 3 | 70 | 0.74 | 0.97 | 18 | empty |
| 4 | 66 | 0.73 | 0.97 | 19 | empty |
| 5 | 634 | 0.72 | 0.80 | 56 | empty |
Interfaces
13 interfaces between chains.
- A–C · 1126 Ų buried · 11 hydrogen bonds · protein-protein
- F–H · 1099 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 1033 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1014 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 693 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4BSS · Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal… · the same entry in another collection · chain H against H, 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 F against A, TM-score 0.98
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 4BSS · PDBe 4BSS · UniProt O75473 · UniProt Q2MKA7
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