Research workbench
Crystal structure of human CALCIUM/CALMODULIN-dependent protein kinase iib isoform 1 (CAMK2B)
Analyse Crystal structure of human CALCIUM/CALMODULIN-dependent protein kinase iib… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BHH
- Type
- protein
- Length
- 1,149 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent protein kinase type II beta chain
- EC
- 2.7.11.17
- UniProt
- Q13554
- Ligands
- 5CP
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALCIUM/CALMODULIN-dependent protein kinase type II beta chain (EC 2.7.11.17) | protein | 289 | 40% helix, 17% strand | Q13554 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II beta chain (EC 2.7.11.17) | protein | 289 | 39% helix, 17% strand | Q13554 |
| C | CALCIUM/CALMODULIN-dependent protein kinase type II beta chain (EC 2.7.11.17) | protein | 285 | 41% helix, 16% strand | Q13554 |
| D | CALCIUM/CALMODULIN-dependent protein kinase type II beta chain (EC 2.7.11.17) | protein | 286 | 40% helix, 16% strand | Q13554 |
Ligands and binding sites
- 5CP · [4-({4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-6-(methylamino)pyrimidin-2-yl}amino)phenyl]acetonitrile · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.76 | 0.82 | 77 | empty |
| 2 | 697 | 0.75 | 0.81 | 63 | empty |
| 3 | 289 | 0.70 | 0.84 | 32 | empty |
| 4 | 292 | 0.59 | 0.78 | 37 | 5CP |
| 5 | 195 | 0.56 | 0.79 | 27 | 5CP |
Interfaces
6 interfaces between chains.
- A–C · 549 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 540 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 255 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3BHH · Crystal structure of human calcium/calmodulin-dependent protein kinase IIB isoform 1… · the same entry in another collection · chain D against D, TM-score 1.00
- Q13554 · AlphaFold monomer V2.0 prediction for CALCIUM/CALMODULIN-dependent protein kinase type II… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q13554
- Elsewhere: RCSB PDB 3BHH · PDBe 3BHH · UniProt Q13554
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