Research workbench
Catalytic domain of human zip kinase phosphorylated at THR265
Analyse Catalytic domain of human zip kinase phosphorylated at THR265 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YRP
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death-associated protein kinase 3
- EC
- 2.7.1.37
- UniProt
- O43293
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Death-associated protein kinase 3 (EC 2.7.1.37) | protein | 276 | 33% helix, 19% strand | O43293 |
Ligands and binding sites
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1022 | 0.87 | 0.88 | 112 | DTT |
| 2 | 74 | 0.45 | 0.82 | 18 | empty |
| 3 | 73 | 0.43 | 0.81 | 17 | empty |
| 4 | 73 | 0.30 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1759 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1YRP · Catalytic domain of human ZIP kinase phosphorylated at Thr265 · the same entry in another collection · chain A against A, TM-score 1.00
- O43293 · AlphaFold monomer V2.0 prediction for death-associated protein kinase 3 (O43293) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 O43293
- Elsewhere: RCSB PDB 1YRP · PDBe 1YRP · UniProt O43293
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