MolNFT v1 · #161067 · protein
Cryo-EM structure of RET/GFRA2/NRTN extracellular complex. the 3D refinement was applied with C2 symmetry.
6Q2O · Neurturin: “Cryo-EM structure of RET/GFRA2/NRTN extracellular complex. the 3D refinement was applied with C2 symmetry.”. Electron microscopy, 2 ligands (NAG, CA), 20 pockets (best druggability 0.85). MolNFT v1 #161067 on GenesisL1…
- PDB
- 6Q2O
- Type
- protein
- Length
- 1,900 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurturin; Gdnf family receptor alpha-2; Proto-oncogene tyrosine-protein kinase receptor…
- EC
- 2.7.10.1
- UniProt
- Q99748, O00451, P07949
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurturin | protein | 98 | 14% helix, 35% strand | Q99748 |
| C, D | Gdnf family receptor alpha-2 | protein | 280 | 52% helix, 3% strand | O00451 |
| E, F | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 572 | 8% helix, 39% strand | P07949 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains E, C, F, D
- 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.85 | 0.85 | 93 | empty |
| 2 | 1001 | 0.84 | 0.85 | 88 | empty |
| 3 | 162 | 0.80 | 0.96 | 28 | empty |
| 4 | 152 | 0.79 | 0.95 | 28 | empty |
| 5 | 375 | 0.63 | 0.78 | 37 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2085 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 1098 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1094 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 892 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 889 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q2O · Cryo-EM structure of RET/GFRa2/NRTN extracellular complex. The 3D refinement was applied… · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.99
- O00451 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-2 (O00451) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q99748 · AlphaFold monomer V2.0 prediction for neurturin (Q99748) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 Q99748
- Every structure of UniProt O00451
- Every structure of UniProt P07949
- Elsewhere: RCSB PDB 6Q2O · PDBe 6Q2O · UniProt Q99748 · UniProt O00451 · UniProt P07949
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