MolNFT v1 · #172715 · protein
Crystal structure of a gdnf-GFRALPHA1 complex
7AB8 · Gdnf family receptor alpha: “Crystal structure of a gdnf-GFRALPHA1 complex”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.35). MolNFT v1 #172715 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7AB8
- Type
- protein
- Length
- 307 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gdnf family receptor alpha; Glial cell line-derived neurotrophic factor
- UniProt
- Q98TT9, Q98TU0
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gdnf family receptor alpha | protein | 209 | 54% helix, 6% strand | Q98TT9 |
| B | Glial cell line-derived neurotrophic factor | protein | 98 | 19% helix, 37% strand | Q98TU0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.35 | 0.76 | 17 | EDO, PEG |
Interfaces
1 interface between chains.
- A–B · 867 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7AB8 · Crystal structure of a GDNF-GFRalpha1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q98TU0 · AlphaFold monomer V2.0 prediction for glial cell line-derived neurotrophic factor (Q98TU0) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q98TT9
- Every structure of UniProt Q98TU0
- Elsewhere: RCSB PDB 7AB8 · PDBe 7AB8 · UniProt Q98TT9 · UniProt Q98TU0
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