Research workbench
Cad domain of PFF0520W, calcium dependent protein kinase
Analyse Cad domain of PFF0520W, calcium dependent protein kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PM8
- Type
- protein
- Length
- 339 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcium-dependent protein kinase 2
- EC
- 2.7.11.1
- UniProt
- O15865
- Ligands
- CA, NA, CL
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcium-dependent protein kinase 2 (EC 2.7.11.1) | protein | 165 | 64% helix, 5% strand | O15865 |
| B | Calcium-dependent protein kinase 2 (EC 2.7.11.1) | protein | 174 | 65% helix, 5% strand | O15865 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.73 | 0.77 | 88 | empty |
| 2 | 135 | 0.64 | 0.87 | 30 | empty |
| 3 | 52 | 0.28 | 0.75 | 16 | NA |
| 4 | 53 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 963 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3PM8 · CAD domain of PFF0520w, Calcium dependent protein kinase · the same entry in another collection · chain A against A, TM-score 1.00
- O15865 · AlphaFold monomer V2.0 prediction for calcium-dependent protein kinase 2 (O15865) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 O15865
- Elsewhere: RCSB PDB 3PM8 · PDBe 3PM8 · UniProt O15865
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