Research workbench
Calcium-dependent protein kinase 1 from toxoplasma gondii (TGCDPK1) in complex with bumped kinase inhibitor na-PP2
Analyse Calcium-dependent protein kinase 1 from toxoplasma gondii (TGCDPK1) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I7C
- Type
- protein
- Length
- 462 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-domain protein kinase 1
- EC
- 2.7.11.17
- UniProt
- Q9BJF5
- Ligands
- BK2
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-domain protein kinase 1 (EC 2.7.11.17) | protein | 462 | 54% helix, 13% strand | Q9BJF5 |
Ligands and binding sites
- BK2 · 1-tert-butyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.83 | 0.84 | 144 | BK2 |
| 2 | 140 | 0.49 | 0.78 | 28 | empty |
| 3 | 93 | 0.37 | 0.76 | 17 | empty |
| 4 | 58 | 0.31 | 0.76 | 14 | empty |
| 5 | 67 | 0.28 | 0.72 | 12 | empty |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3I7C · Calcium-Dependent Protein Kinase 1 from Toxoplasma gondii (TgCDPK1) in complex with… · 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 3I7C · PDBe 3I7C · UniProt Q9BJF5
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