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
- 5MR5
- Type
- protein
- Length
- 592 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
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurturin | protein | 98 | 14% helix, 40% strand | Q99748 |
| C, D | Gdnf family receptor alpha-2 | protein | 198 | 61% helix, 5% strand | O00451 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.40 | 0.82 | 16 | empty |
| 2 | 73 | 0.40 | 0.79 | 19 | empty |
| 3 | 54 | 0.34 | 0.78 | 18 | GOL |
| 4 | 51 | 0.33 | 0.78 | 19 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1995 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 836 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 833 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide (disulfide).
Compared structures
- 5MR5 · 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 0.99
- Q99748 · AlphaFold monomer V2.0 prediction for neurturin (Q99748) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 5MR5 · PDBe 5MR5 · UniProt Q99748 · UniProt O00451
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