Research workbench
Crystal structure of the human KLHL3 kelch domain in complex with a WNK3 peptide
Analyse Crystal structure of the human KLHL3 kelch domain in complex with a WNK3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NKP
- Type
- protein
- Length
- 596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kelch-like protein 3; SERINE/THREONINE-protein kinase WNK3
- EC
- 2.7.11.1
- UniProt
- Q9UH77, Q9BYP7
- Ligands
- CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kelch-like protein 3 | protein | 286 | 0% helix, 52% strand | Q9UH77 |
| B | Kelch-like protein 3 | protein | 289 | 0% helix, 49% strand | Q9UH77 |
| D | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 10 | 40% helix, 0% strand | Q9BYP7 |
| C | SERINE/THREONINE-protein kinase WNK3 (EC 2.7.11.1) | protein | 11 | 36% helix, 0% strand | Q9BYP7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.74 | 0.84 | 38 | empty |
| 2 | 385 | 0.73 | 0.84 | 37 | empty |
| 3 | 110 | 0.57 | 0.85 | 26 | empty |
| 4 | 124 | 0.40 | 0.75 | 23 | empty |
| 5 | 84 | 0.38 | 0.77 | 21 | CL |
Interfaces
3 interfaces between chains.
- B–C · 648 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 600 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5NKP · Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UH77 · AlphaFold monomer V2.0 prediction for kelch-like protein 3 (Q9UH77) · a predicted model of the same protein · 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 D against A, TM-score 0.59
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 Q9UH77
- Every structure of UniProt Q9BYP7
- Elsewhere: RCSB PDB 5NKP · PDBe 5NKP · UniProt Q9UH77 · UniProt Q9BYP7
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