Research workbench
Crystal structure of CDPK1 of toxoplasma gondii, TGME49_101440, in presence of calcium
Analyse Crystal structure of CDPK1 of toxoplasma gondii, TGME49_101440, in presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HX4
- Type
- protein
- Length
- 467 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-domain protein kinase 1
- UniProt
- Q9BJF5
- Ligands
- ANP, CA, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-domain protein kinase 1 | protein | 467 | 46% helix, 12% strand | Q9BJF5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.69 | 0.78 | 67 | empty |
| 2 | 300 | 0.66 | 0.82 | 37 | ANP, GOL |
| 3 | 53 | 0.35 | 0.79 | 14 | empty |
| 4 | 54 | 0.35 | 0.79 | 16 | empty |
| 5 | 87 | 0.34 | 0.74 | 13 | empty |
Compared structures
- 3HX4 · Crystal structure of CDPK1 of Toxoplasma gondii, TGME49_101440, in presence of calcium · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9BJF5
- Elsewhere: RCSB PDB 3HX4 · PDBe 3HX4 · UniProt Q9BJF5
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