MolNFT v1 · #143415 · protein
The structure of human camkii with bound inhibitor
6AYW · CALCIUM/CALMODULIN-dependent protein kinase type II subunit…: “The structure of human camkii with bound inhibitor”. X-ray diffraction, 1 ligand (C2V), 5 pockets (best druggability 0.73). MolNFT v1 #143415 on GenesisL1: 3D structure…
- PDB
- 6AYW
- Type
- protein
- Length
- 586 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
- C2V
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 293 | 43% helix, 18% strand | Q13557 |
| B | CALCIUM/CALMODULIN-dependent protein kinase type II subunit delta (EC 2.7.11.17) | protein | 293 | 42% helix, 17% strand | Q13557 |
Ligands and binding sites
- C2V · N-[2-(dimethylamino)ethyl]-3-[6-(thiophen-2-yl) imidazo[1,2-b]pyridazin-3-yl]benzamide · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.73 | 0.76 | 99 | C2V |
| 2 | 434 | 0.72 | 0.82 | 41 | C2V |
| 3 | 206 | 0.56 | 0.79 | 23 | empty |
| 4 | 91 | 0.40 | 0.78 | 26 | empty |
| 5 | 85 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 598 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AYW · 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 6AYW · PDBe 6AYW · UniProt Q13557
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