Research workbench
Crystal structure of WNK3 kinase domain in a monophosphorylated apo state
Analyse Crystal structure of WNK3 kinase domain in a monophosphorylated apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O23
- Type
- protein
- Length
- 549 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
- SO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 270 | 41% helix, 18% strand | Q9BYP7 |
| B | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 279 | 42% helix, 20% strand | Q9BYP7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 28 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.83 | 0.84 | 134 | SO4, EDO |
| 2 | 57 | 0.39 | 0.80 | 13 | EDO |
| 3 | 72 | 0.37 | 0.77 | 13 | EDO |
| 4 | 53 | 0.34 | 0.78 | 15 | empty |
| 5 | 60 | 0.33 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5O23 · Crystal structure of WNK3 kinase domain in a monophosphorylated apo state · 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 B against A, TM-score 0.93
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 5O23 · PDBe 5O23 · UniProt Q9BYP7
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