MolNFT v1 · #97723 · protein
Crystal structure of human LGR5-RSPO1-RNF43
4KNG · Leucine-rich repeat-containing G-protein coupled receptor 5: “Crystal structure of human LGR5-RSPO1-RNF43”. X-ray diffraction, 2 ligands (NAG, NI), 18 pockets (best druggability 0.80). MolNFT v1 #97723 on GenesisL1: 3D structure…
- PDB
- 4KNG
- Type
- protein
- Length
- 1,413 residues
- Chains
- 6
- 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; E3…
- EC
- 6.3.2.-
- UniProt
- O75473, Q2MKA7, Q68DV7
- Ligands
- NAG, NI
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 461 | 3% helix, 18% strand | O75473 |
| B | Leucine-rich repeat-containing G-protein coupled receptor 5 | protein | 463 | 4% helix, 19% strand | O75473 |
| M | R-spondin-1 | protein | 98 | 0% helix, 44% strand | Q2MKA7 |
| P | R-spondin-1 | protein | 94 | 0% helix, 46% strand | Q2MKA7 |
| E | E3 ubiquitin-protein ligase RNF43 (EC 6.3.2.-) | protein | 149 | 19% helix, 30% strand | Q68DV7 |
| F | E3 ubiquitin-protein ligase RNF43 (EC 6.3.2.-) | protein | 148 | 18% helix, 29% strand | Q68DV7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.80 | 0.84 | 84 | empty |
| 2 | 1079 | 0.79 | 0.81 | 117 | empty |
| 3 | 82 | 0.76 | 0.97 | 24 | empty |
| 4 | 71 | 0.76 | 0.98 | 20 | empty |
| 5 | 263 | 0.71 | 0.85 | 35 | empty |
Interfaces
12 interfaces between chains.
- M–E · 1191 Ų buried · 23 hydrogen bonds · protein-protein
- P–F · 1129 Ų buried · 19 hydrogen bonds · protein-protein
- A–M · 1114 Ų buried · 9 hydrogen bonds · protein-protein
- B–P · 1003 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 497 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4KNG · Crystal structure of human LGR5-RSPO1-RNF43 · the same entry in another collection · chain F against F, 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
- Q68DV7 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF43 (Q68DV7) · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q2MKA7 · AlphaFold monomer V2.0 prediction for R-spondin-1 (Q2MKA7) · a predicted model of the same protein · chain P 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
- Every structure of UniProt Q68DV7
- Elsewhere: RCSB PDB 4KNG · PDBe 4KNG · UniProt O75473 · UniProt Q2MKA7 · UniProt Q68DV7
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