Research workbench
Crystal structure of phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018366
Analyse Crystal structure of phosphorylated RET V804M tyrosine kinase domain complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I83
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.88
- Source
- Homo sapiens
- Molecule
- Proto-oncogene tyrosine-protein kinase receptor Ret
- EC
- 2.7.10.1
- UniProt
- P07949
- Ligands
- H72
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · resolution 1.88 · 1 distinct chain · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase receptor Ret (EC 2.7.10.1) | protein | 292 | 42% helix, 22% strand | P07949 |
Ligands and binding sites
- H72 · 4-[5-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-3-yl]benzamide · ligand · chains A
- FMT · Formic acid · additive · 15 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.59 | 0.84 | 22 | H72 |
| 2 | 66 | 0.58 | 0.89 | 20 | empty |
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6I83 · Crystal structure of phosphorylated ret V804M tyrosine kinase domain complexed with… · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.93
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 P07949
- Elsewhere: RCSB PDB 6I83 · PDBe 6I83 · UniProt P07949
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