Research workbench
Crystal structure of JAK3 kinase domain in complex with compound 25
Analyse Crystal structure of JAK3 kinase domain in complex with compound 25 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UYV
- Type
- protein
- Length
- 1,115 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase JAK3
- EC
- 2.7.10.2
- UniProt
- P52333
- Ligands
- OV5, CL
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 278 | 41% helix, 20% strand | P52333 |
| B | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 284 | 43% helix, 19% strand | P52333 |
| C | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 281 | 43% helix, 20% strand | P52333 |
| D | Tyrosine-protein kinase JAK3 (EC 2.7.10.2) | protein | 272 | 42% helix, 21% strand | P52333 |
Ligands and binding sites
- OV5 · 6-{[(2M)-2-(2-chloro-6-fluorophenyl)-5-oxo-5H-pyrrolo[3,4-b]pyridin-4-yl]amino}-N-ethylpyridine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.79 | 0.81 | 72 | OV5 |
| 2 | 894 | 0.76 | 0.79 | 80 | OV5 |
| 3 | 669 | 0.71 | 0.78 | 53 | OV5 |
| 4 | 438 | 0.66 | 0.79 | 38 | OV5 |
| 5 | 404 | 0.63 | 0.78 | 36 | empty |
Interfaces
3 interfaces between chains.
- C–D · 795 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 784 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (phosphorylation).
Compared structures
- 7UYV · Crystal structure of JAK3 kinase domain in complex with compound 25 · the same entry in another collection · chain D against D, TM-score 1.00
- P52333 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase JAK3 (P52333) · a predicted model of the same protein · chain D 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 P52333
- Elsewhere: RCSB PDB 7UYV · PDBe 7UYV · UniProt P52333
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