Research workbench
Structure of pragmin pseudo-kinase reveals a dimerization mechanism to regulate protein tyrosine phosphorylation and nuclear transcription
Analyse Structure of pragmin pseudo-kinase reveals a dimerization mechanism to regulate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EWX
- Type
- protein
- Length
- 717 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PEAK1-related kinase-activating pseudokinase 1
- UniProt
- D3ZMK9
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PEAK1-related kinase-activating pseudokinase 1 | protein | 359 | 48% helix, 14% strand | D3ZMK9 |
| B | PEAK1-related kinase-activating pseudokinase 1 | protein | 358 | 47% helix, 11% strand | D3ZMK9 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.52 | 0.75 | 34 | empty |
| 2 | 74 | 0.47 | 0.83 | 19 | empty |
| 3 | 109 | 0.44 | 0.77 | 20 | empty |
| 4 | 73 | 0.40 | 0.79 | 15 | empty |
| 5 | 123 | 0.39 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2035 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6EWX · Structure of Pragmin pseudo-kinase reveals a dimerization mechanism to regulate protein… · the same entry in another collection · chain A against A, TM-score 1.00
- D3ZMK9 · AlphaFold monomer V2.0 prediction for inactive tyrosine-protein kinase PRAG1 (D3ZMK9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 D3ZMK9
- Elsewhere: RCSB PDB 6EWX · PDBe 6EWX · UniProt D3ZMK9
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