Research workbench
Cryo-EM structure of RET/GFRA3/ARTN extracellular complex. the 3D refinement was applied with C2 symmetry.
Analyse Cryo-EM structure of RET/GFRA3/ARTN extracellular complex. the 3D refinement… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q2S
- Type
- protein
- Length
- 1,734 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein SMT3,ARTEMIN; Gdnf family receptor alpha-3; Proto-oncogene…
- EC
- 2.7.10.1
- UniProt
- Q12306, Q5T4W7, O60609, P07949
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin-like protein SMT3,ARTEMIN | protein | 98 | 12% helix, 39% strand | Q12306, Q5T4W7 |
| C, D | Gdnf family receptor alpha-3 | protein | 199 | 55% helix, 3% strand | O60609 |
| E, F | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 570 | 6% helix, 39% strand | P07949 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains C, E, D, F
- 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.81 | 0.83 | 70 | empty |
| 2 | 366 | 0.80 | 0.89 | 43 | empty |
| 3 | 1057 | 0.79 | 0.81 | 84 | empty |
| 4 | 389 | 0.79 | 0.88 | 49 | empty |
| 5 | 314 | 0.60 | 0.78 | 48 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1634 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 949 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 948 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 820 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 818 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q2S · Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied… · the same entry in another collection · chain F against F, TM-score 1.00
- O60609 · AlphaFold monomer V2.0 prediction for gdnf family receptor alpha-3 (O60609) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q5T4W7 · AlphaFold monomer V2.0 prediction for artemin (Q5T4W7) · a predicted model of the same protein · chain A 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 0.95
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 Q12306
- Every structure of UniProt Q5T4W7
- Every structure of UniProt O60609
- Every structure of UniProt P07949
- Elsewhere: RCSB PDB 6Q2S · PDBe 6Q2S · UniProt Q12306 · UniProt Q5T4W7 · UniProt O60609 · UniProt P07949
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