MolNFT v1 · #128813 · protein
Crystal structure of WNK3 kinase domain in a monophosphorylated apo state (a-loop swapped)
5O1V · SERINE/THREONINE-protein kinase WNK3: “Crystal structure of WNK3 kinase domain in a monophosphorylated apo state (a-loop swapped)”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #128813 on GenesisL1: 3D structure…
- PDB
- 5O1V
- Type
- protein
- Length
- 550 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
- Pockets
- 6 · best druggability 0.75
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 | 279 | 39% helix, 20% strand | Q9BYP7 |
| B | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 271 | 38% helix, 21% strand | Q9BYP7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.75 | 0.78 | 100 | EDO |
| 2 | 345 | 0.74 | 0.85 | 49 | EDO |
| 3 | 257 | 0.70 | 0.85 | 33 | EDO |
| 4 | 69 | 0.35 | 0.77 | 18 | empty |
| 5 | 52 | 0.35 | 0.79 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2026 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 5O1V · Crystal structure of WNK3 kinase domain in a monophosphorylated apo state (A-loop swapped) · 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 0.89
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 5O1V · PDBe 5O1V · UniProt Q9BYP7
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