Research workbench
Crystal structure of kinase domain of TGCDPK1 in presence of 3BRB-PP1
Analyse Crystal structure of kinase domain of TGCDPK1 in presence of 3BRB-PP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MA6
- Type
- protein
- Length
- 533 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-domain protein kinase 1
- UniProt
- Q9BJF5
- Ligands
- DXR
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-domain protein kinase 1 | protein | 267 | 39% helix, 16% strand | Q9BJF5 |
| B | Calmodulin-domain protein kinase 1 | protein | 266 | 39% helix, 18% strand | Q9BJF5 |
Ligands and binding sites
- DXR · 3-(3-bromobenzyl)-1-tert-butyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.82 | 0.83 | 106 | DXR |
| 2 | 520 | 0.75 | 0.82 | 71 | DXR |
| 3 | 280 | 0.65 | 0.82 | 33 | empty |
| 4 | 154 | 0.57 | 0.82 | 19 | empty |
| 5 | 59 | 0.39 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 973 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3MA6 · Crystal structure of kinase domain of TgCDPK1 in presence of 3BrB-PP1 · 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 3MA6 · PDBe 3MA6 · UniProt Q9BJF5
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