MolNFT v1 · #108123 · protein
Ret recognition of gdnf-GFRALPHA1 ligand by a composite binding site promotes membrane-proximal self-association
4UX8 · Proto-oncogene tyrosine-protein kinase receptor ret: “Ret recognition of gdnf-GFRALPHA1 ligand by a composite binding site promotes membrane-proximal…”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.73).…
- PDB
- 4UX8
- Type
- protein
- Length
- 1,650 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase receptor ret; Gdnf family receptor alpha-1; Glial…
- EC
- 2.7.10.1
- UniProt
- P07949, O35748, P39905
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 26% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 448 | 8% helix, 37% strand | P07949 |
| C, E | Gdnf family receptor alpha-1 | protein | 284 | 58% helix, 2% strand | O35748 |
| D, F | Glial cell line-derived neurotrophic factor | protein | 93 | 15% helix, 39% strand | P39905 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains D, F
- CA · Calcium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.73 | 0.76 | 99 | empty |
| 2 | 53 | 0.69 | 0.97 | 17 | empty |
| 3 | 325 | 0.60 | 0.77 | 50 | empty |
| 4 | 189 | 0.58 | 0.81 | 38 | empty |
| 5 | 215 | 0.57 | 0.79 | 40 | empty |
Interfaces
5 interfaces between chains.
- D–F · 1608 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 865 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 862 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 340 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4UX8 · RET recognition of GDNF-GFRalpha1 ligand by a composite binding site promotes… · the same entry in another collection · chain F against F, TM-score 1.00
- P39905 · AlphaFold monomer V2.0 prediction for glial cell line-derived neurotrophic factor (P39905) · a predicted model of the same protein · chain D against A, TM-score 0.94
- P07949 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase receptor ret… · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P07949
- Every structure of UniProt O35748
- Every structure of UniProt P39905
- Elsewhere: RCSB PDB 4UX8 · PDBe 4UX8 · UniProt P07949 · UniProt O35748 · UniProt P39905
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