MolNFT v1 · #123919 · protein
Crystal structure of DCLK1-kd in complex with amppn
5JZJ · SERINE/THREONINE-protein kinase DCLK1: “Crystal structure of DCLK1-kd in complex with amppn”. X-ray diffraction, 3 ligands (AN2, MG, SO4), 4 pockets (best druggability 0.85). MolNFT v1 #123919 on GenesisL1: 3D structure, binding…
- PDB
- 5JZJ
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase DCLK1
- EC
- 2.7.11.1
- UniProt
- O15075
- Ligands
- AN2, MG, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 271 | 33% helix, 22% strand | O15075 |
| B | SERINE/THREONINE-protein kinase DCLK1 (EC 2.7.11.1) | protein | 261 | 35% helix, 22% strand | O15075 |
Ligands and binding sites
- AN2 · Amp phosphoramidate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.85 | 0.86 | 109 | MG, SO4, AN2 |
| 2 | 263 | 0.56 | 0.77 | 40 | empty |
| 3 | 177 | 0.50 | 0.77 | 22 | empty |
| 4 | 108 | 0.43 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1701 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5JZJ · Crystal structure of DCLK1-KD in complex with AMPPN · the same entry in another collection · chain A against A, TM-score 1.00
- O15075 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase DCLK1 (O15075) · 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 O15075
- Elsewhere: RCSB PDB 5JZJ · PDBe 5JZJ · UniProt O15075
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