Research workbench
Crystal structure of WNK1 in complex with MN2+AMPPNP and WNK476
Analyse Crystal structure of WNK1 in complex with MN2+AMPPNP and WNK476 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TF9
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase WNK1
- EC
- 2.7.11.1
- UniProt
- Q9H4A3
- Ligands
- 7AV, ANP, MN, CA
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase WNK1 (EC 2.7.11.1) | protein | 262 | 37% helix, 21% strand | Q9H4A3 |
| B | SERINE/THREONINE-protein kinase WNK1 (EC 2.7.11.1) | protein | 266 | 35% helix, 21% strand | Q9H4A3 |
Ligands and binding sites
- 7AV · {2-[(4-chlorophenyl)methoxy]phenyl}{5-[2-(methylamino)-1,3-thiazol-4-yl]-2,3-dihydro-1H-indol-1-yl}methanone · ligand · 2 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
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 | 754 | 0.74 | 0.79 | 60 | 7AV, ANP, MN |
| 2 | 780 | 0.74 | 0.79 | 60 | 7AV, ANP, MN |
| 3 | 247 | 0.53 | 0.76 | 23 | empty |
| 4 | 61 | 0.50 | 0.85 | 18 | empty |
| 5 | 53 | 0.35 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1870 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5TF9 · Crystal structure of WNK1 in complex with Mn2+AMPPNP and WNK476 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H4A3 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase WNK1 (Q9H4A3) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q9H4A3
- Elsewhere: RCSB PDB 5TF9 · PDBe 5TF9 · UniProt Q9H4A3
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