Research workbench
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
- 6BAB
- Type
- protein
- Length
- 1,150 residues
- Chains
- 4
- 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
- Q6PHZ2
- Ligands
- D0S
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 18% 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 | 41% helix, 19% strand | Q6PHZ2 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta (EC 2.7.11.17) | protein | 285 | 41% helix, 17% strand | Q6PHZ2 |
| C | CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta (EC 2.7.11.17) | protein | 284 | 43% helix, 18% strand | Q6PHZ2 |
| D | CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta (EC 2.7.11.17) | protein | 291 | 41% helix, 18% strand | Q6PHZ2 |
Ligands and binding sites
- D0S · N-[(2S)-2-(diethylamino)propyl]-2-(3-hydroxyazetidin-1-yl)-6-[5-(thiophen-2-yl)pyrazolo[1,5-a]pyrimidin-3-yl]pyridine-4-carboxamide · ligand · 4 copies · chains A, B, C, D
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.78 | 0.80 | 88 | TLA |
| 2 | 752 | 0.77 | 0.82 | 73 | D0S |
| 3 | 930 | 0.76 | 0.79 | 80 | D0S |
| 4 | 833 | 0.75 | 0.79 | 84 | D0S |
| 5 | 209 | 0.64 | 0.83 | 28 | D0S |
Interfaces
4 interfaces between chains.
- B–C · 819 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 681 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 675 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 405 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6BAB · The structure of human CamKII with bound inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- Q6PHZ2 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type II… · a predicted model of the same protein · chain D 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 Q6PHZ2
- Elsewhere: RCSB PDB 6BAB · PDBe 6BAB · UniProt Q6PHZ2
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