MolNFT v1 · #64128 · protein
Crystal structure of gdnf-GFRALPHA1 complex
3FUB · Gdnf family receptor alpha-1: “Crystal structure of gdnf-GFRALPHA1 complex”. X-ray diffraction, 2 ligands (NAG, SO4), 5 pockets (best druggability 0.74). MolNFT v1 #64128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FUB
- Type
- protein
- Length
- 593 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gdnf family receptor alpha-1; Glial cell line-derived neurotrophic factor
- UniProt
- Q62997, P39905
- Ligands
- NAG, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Gdnf family receptor alpha-1 | protein | 199 | 60% helix, 4% strand | Q62997 |
| B | Glial cell line-derived neurotrophic factor | protein | 92 | 16% helix, 39% strand | P39905 |
| D | Glial cell line-derived neurotrophic factor | protein | 103 | 14% helix, 35% strand | P39905 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, B
- SO4 · Sulfate ion · ion · chains C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.74 | 0.77 | 94 | empty |
| 2 | 117 | 0.47 | 0.79 | 17 | empty |
| 3 | 102 | 0.37 | 0.75 | 17 | empty |
| 4 | 70 | 0.34 | 0.76 | 17 | empty |
| 5 | 54 | 0.26 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 864 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 855 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 560 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 26 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3FUB · Crystal structure of GDNF-GFRalpha1 complex · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.95
- Q62997 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-1 (Q62997) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q62997
- Every structure of UniProt P39905
- Elsewhere: RCSB PDB 3FUB · PDBe 3FUB · UniProt Q62997 · UniProt P39905
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