Research workbench
Glial cell-derived neurotrophic factor from rat
Analyse Glial cell-derived neurotrophic factor from rat in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AGQ
- Type
- protein
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glial cell-derived neurotrophic factor
- UniProt
- Q07731
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glial cell-derived neurotrophic factor | protein | 91 | 18% helix, 40% strand | Q07731 |
| B | Glial cell-derived neurotrophic factor | protein | 96 | 16% helix, 38% strand | Q07731 |
| C | Glial cell-derived neurotrophic factor | protein | 91 | 16% helix, 40% strand | Q07731 |
| D | Glial cell-derived neurotrophic factor | protein | 95 | 16% helix, 38% strand | Q07731 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.41 | 0.75 | 33 | empty |
| 2 | 59 | 0.34 | 0.77 | 11 | empty |
| 3 | 72 | 0.32 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1469 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1461 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 345 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 1AGQ · Glial cell-derived neurotrophic factor from rat · the same entry in another collection · chain D against D, TM-score 1.00
- Q07731 · AlphaFold monomer V2.0 prediction for glial cell line-derived neurotrophic factor (Q07731) · a predicted model of the same protein · chain A 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 Q07731
- Elsewhere: RCSB PDB 1AGQ · PDBe 1AGQ · UniProt Q07731
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