MolNFT v1 · #128824 · protein
Crystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/MG2+
5O26 · SERINE/THREONINE-protein kinase WNK3: “Crystal structure of WNK3 kinase domain in a diphosphorylated state and in complex with AMP-PNP/MG2+”. X-ray diffraction, 2 ligands (ANP, MG), 5 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5O26
- Type
- protein
- Length
- 540 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
- ANP, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 273 | 38% helix, 22% strand | Q9BYP7 |
| B | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 267 | 37% helix, 21% strand | Q9BYP7 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 711 | 0.72 | 0.79 | 74 | ANP, MG |
| 2 | 202 | 0.54 | 0.78 | 27 | empty |
| 3 | 219 | 0.52 | 0.76 | 34 | ANP, MG |
| 4 | 50 | 0.31 | 0.77 | 13 | empty |
| 5 | 51 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 479 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5O26 · Crystal structure of WNK3 kinase domain in a diphosphorylated state and in 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 0.91
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 5O26 · PDBe 5O26 · UniProt Q9BYP7
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