Research workbench
Ligand-receptor complex.
Analyse Ligand-receptor complex. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MR4
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurturin; Gdnf family receptor alpha-2
- UniProt
- Q99748, O00451
- Pockets
- 8 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurturin | protein | 98 | 15% helix, 39% strand | Q99748 |
| C | Gdnf family receptor alpha-2 | protein | 285 | 58% helix, 4% strand | O00451 |
| D | Gdnf family receptor alpha-2 | protein | 285 | 59% helix, 4% strand | O00451 |
Ligands and binding sites
- FMT · Formic acid · additive · 3 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.47 | 0.81 | 15 | empty |
| 2 | 73 | 0.42 | 0.80 | 20 | FMT |
| 3 | 137 | 0.42 | 0.75 | 25 | empty |
| 4 | 78 | 0.32 | 0.75 | 15 | empty |
| 5 | 52 | 0.31 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2180 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 874 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 838 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide (disulfide).
Compared structures
- 5MR4 · Ligand-receptor complex. · the same entry in another collection · chain A against A, TM-score 1.00
- O00451 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-2 (O00451) · a predicted model of the same protein · chain C against A, TM-score 0.96
- Q99748 · AlphaFold monomer V2.0 prediction for neurturin (Q99748) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 Q99748
- Every structure of UniProt O00451
- Elsewhere: RCSB PDB 5MR4 · PDBe 5MR4 · UniProt Q99748 · UniProt O00451
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