Research workbench
JAK2 JH1 in complex with PN4-073
Analyse JAK2 JH1 in complex with PN4-073 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VNK
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Tyrosine-protein kinase JAK2
- EC
- 2.7.10.2
- UniProt
- O60674
- Ligands
- RXT
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 289 | 45% helix, 19% strand | O60674 |
| B, A | Tyrosine-protein kinase JAK2 (EC 2.7.10.2) | protein | 297 | 44% helix, 19% strand | O60674 |
Ligands and binding sites
- RXT · (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile · ligand · 4 copies · chains D, B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.84 | 0.86 | 96 | RXT |
| 2 | 958 | 0.80 | 0.81 | 94 | RXT |
| 3 | 515 | 0.75 | 0.83 | 59 | empty |
| 4 | 380 | 0.70 | 0.82 | 56 | RXT |
| 5 | 398 | 0.68 | 0.81 | 46 | RXT |
Interfaces
3 interfaces between chains.
- B–A · 1141 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 524 Ų buried · 9 hydrogen bonds · protein-protein
- D–B · 504 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6VNK · JAK2 JH1 in complex with PN4-073 · the same entry in another collection · chain A against A, TM-score 1.00
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 O60674
- Elsewhere: RCSB PDB 6VNK · PDBe 6VNK · UniProt O60674
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