Research workbench
Cryo-EM structure of RET/GFRA2/NRTN extracellular complex in the tetrameric form
Analyse Cryo-EM structure of RET/GFRA2/NRTN extracellular complex in the tetrameric form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q2R
- Type
- protein
- Length
- 3,800 residues
- Chains
- 12
- 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 0.86
Structure
electron microscopy · 3 distinct chains · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, U, V | Neurturin | protein | 98 | 15% helix, 36% strand | Q99748 |
| C, D, W, X | Gdnf family receptor alpha-2 | protein | 280 | 55% helix, 3% strand | O00451 |
| E, F, Y, Z | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 572 | 9% helix, 37% strand | P07949 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains E, C, F, D, Y, W, Z, X
- CA · Calcium ion · metal · 16 copies · chains E, F, Y, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.86 | 0.87 | 106 | empty |
| 2 | 983 | 0.83 | 0.85 | 90 | empty |
| 3 | 921 | 0.83 | 0.85 | 84 | empty |
| 4 | 281 | 0.82 | 0.93 | 40 | empty |
| 5 | 287 | 0.81 | 0.92 | 42 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2199 Ų buried · 24 hydrogen bonds · protein-protein
- U–V · 2177 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1156 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1151 Ų buried · 17 hydrogen bonds · protein-protein
- X–Z · 1135 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 106 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q2R · Cryo-EM structure of RET/GFRa2/NRTN extracellular complex in the tetrameric form · the same entry in another collection · chain W against W, TM-score 1.00
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 6Q2R · PDBe 6Q2R · UniProt Q99748 · UniProt O00451 · UniProt P07949
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