Research workbench
Structure of the ectodomain of LGR5 in complex with R-spondin-1 (FU1FU2) in P22121 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
- 4BSR
- Type
- protein
- Length
- 1,170 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 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 483 | 8% helix, 18% strand | O75473 |
| B | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 480 | 8% helix, 18% strand | O75473 |
| C | R-spondin-1 | protein | 103 | 0% helix, 45% strand | Q2MKA7 |
| D | R-spondin-1 | protein | 104 | 0% helix, 40% strand | Q2MKA7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
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 | 1005 | 0.79 | 0.81 | 88 | empty |
| 2 | 64 | 0.75 | 0.98 | 14 | empty |
| 3 | 88 | 0.74 | 0.95 | 19 | empty |
| 4 | 413 | 0.70 | 0.82 | 35 | empty |
| 5 | 454 | 0.70 | 0.81 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1121 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1079 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 560 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 551 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4BSR · Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121… · 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 A 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 D 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 4BSR · PDBe 4BSR · UniProt O75473 · UniProt Q2MKA7
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