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The structure of human camkii with bound inhibitor
Analyse The structure of human camkii with bound inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VLO
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta
- EC
- 2.7.11.17
- UniProt
- Q13557
- Ligands
- 9EJ
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta (EC 2.7.11.17) | protein | 290 | 43% helix, 17% strand | Q13557 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta (EC 2.7.11.17) | protein | 293 | 41% helix, 17% strand | Q13557 |
Ligands and binding sites
- 9EJ · N-[(2S)-2-(diethylamino)propyl]-2-[(2S)-2-(methylcarbamoyl)azetidin-1-yl]-6-[5-(thiophen-2-yl) pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide · ligand · 2 copies · chains A, B
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.71 | 0.77 | 76 | 9EJ |
| 2 | 431 | 0.71 | 0.82 | 38 | 9EJ |
| 3 | 208 | 0.54 | 0.78 | 24 | empty |
| 4 | 95 | 0.39 | 0.76 | 25 | empty |
| 5 | 76 | 0.38 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VLO · The structure of human CamKII with bound inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q13557 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type II… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q13557
- Elsewhere: RCSB PDB 5VLO · PDBe 5VLO · UniProt Q13557
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