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Crystal structure of phosphorylated ret tyrosine kinase domain with inhibitor
Analyse Crystal structure of phosphorylated ret tyrosine kinase domain with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X2M
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase receptor ret
- EC
- 2.7.10.1
- UniProt
- P07949
- Ligands
- X2M
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 287 | 40% helix, 20% strand | P07949 |
| B | Proto-oncogene tyrosine-protein kinase receptor ret (EC 2.7.10.1) | protein | 280 | 40% helix, 18% strand | P07949 |
Ligands and binding sites
- X2M · (3Z)-3-[(3,5-dimethyl-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one · ligand · 2 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.78 | 0.80 | 83 | X2M |
| 2 | 62 | 0.59 | 0.91 | 20 | FMT |
| 3 | 118 | 0.45 | 0.78 | 28 | empty |
| 4 | 123 | 0.44 | 0.77 | 24 | empty |
| 5 | 101 | 0.43 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1449 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2X2M · Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor · 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 B against A, TM-score 0.94
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 2X2M · PDBe 2X2M · UniProt P07949
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