MolNFT v1 · #128829 · protein
Crystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with the inhibitor pp-121
5O2B · SERINE/THREONINE-protein kinase WNK3: “Crystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with the inhibitor pp-121”. X-ray diffraction, 2 ligands (KS1, NA), 4 pockets (best druggability 0.72).…
- PDB
- 5O2B
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase WNK3
- EC
- 2.7.11.1
- UniProt
- Q9BYP7
- Ligands
- KS1, NA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 269 | 40% helix, 20% strand | Q9BYP7 |
| B | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 257 | 38% helix, 23% strand | Q9BYP7 |
Ligands and binding sites
- KS1 · 1-cyclopentyl-3-(1H-pyrrolo[2,3-b]pyridin-5-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.72 | 0.85 | 45 | KS1 |
| 2 | 287 | 0.71 | 0.85 | 46 | KS1 |
| 3 | 85 | 0.34 | 0.74 | 17 | empty |
| 4 | 69 | 0.31 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1403 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5O2B · Crystal structure of WNK3 kinase domain in a diphosphorylated state and in a complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYP7 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase WNK3 (Q9BYP7) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9BYP7
- Elsewhere: RCSB PDB 5O2B · PDBe 5O2B · UniProt Q9BYP7
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