MolNFT v1 · #161066 · protein
Cryo-EM structure of RET/GFRA1/GDNF extracellular complex
6Q2N · Glial cell line-derived neurotrophic factor: “Cryo-EM structure of RET/GFRA1/GDNF extracellular complex”. Electron microscopy, 1 ligand (CA), 20 pockets (best druggability 0.77). MolNFT v1 #161066 on GenesisL1: 3D structure, binding…
- PDB
- 6Q2N
- Type
- protein
- Length
- 1,678 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glial cell line-derived neurotrophic factor; Gdnf family receptor alpha-1; Proto-oncogene…
- EC
- 2.7.10.1
- UniProt
- P39905, P56159, P07949
- Ligands
- CA
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glial cell line-derived neurotrophic factor | protein | 86 | 10% helix, 28% strand | P39905 |
| C, D | Gdnf family receptor alpha-1 | protein | 200 | 59% helix, 3% strand | P56159 |
| E, F | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 553 | 7% helix, 38% strand | P07949 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.77 | 0.95 | 22 | empty |
| 2 | 982 | 0.76 | 0.79 | 79 | empty |
| 3 | 1007 | 0.76 | 0.78 | 80 | empty |
| 4 | 129 | 0.75 | 0.94 | 24 | empty |
| 5 | 576 | 0.73 | 0.80 | 70 | empty |
Interfaces
9 interfaces between chains.
- D–F · 1073 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1041 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1035 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 995 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 948 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide (disulfide).
Compared structures
- 6Q2N · Cryo-EM structure of RET/GFRa1/GDNF extracellular complex · the same entry in another collection · chain F against F, TM-score 1.00
- P56159 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-1 (P56159) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P07949 · AlphaFold monomer V2.0 prediction for proto-oncogene tyrosine-protein kinase receptor ret… · a predicted model of the same protein · chain E against A, TM-score 0.96
- 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 0.85
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 P39905
- Every structure of UniProt P56159
- Every structure of UniProt P07949
- Elsewhere: RCSB PDB 6Q2N · PDBe 6Q2N · UniProt P39905 · UniProt P56159 · UniProt P07949
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