Research workbench
Crystal structure of SU6656-bound CALCIUM/CALMODULIN-dependent protein kinase II delta in complex with calmodulin
Analyse Crystal structure of SU6656-bound CALCIUM/CALMODULIN-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
- 2WEL
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CALCIUM/CALMODULIN-dependent protein kinase type II delta chain; Calmodulin
- EC
- 2.7.11.17
- UniProt
- Q13557, P62158
- Ligands
- K88, CA, PO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CALCIUM/CALMODULIN-dependent protein kinase type II delta chain (EC 2.7.11.17) | protein | 304 | 42% helix, 17% strand | Q13557 |
| D | Calmodulin | protein | 145 | 59% helix, 4% strand | P62158 |
Ligands and binding sites
- K88 · (3Z)-N,N-dimethyl-2-oxo-3-(4,5,6,7-tetrahydro-1H-indol-2-ylmethylidene)-2,3-dihydro-1H-indole-5-sulfonamide · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains D
- PO4 · Phosphate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.64 | 0.78 | 38 | K88, EDO |
| 2 | 188 | 0.52 | 0.78 | 24 | empty |
| 3 | 60 | 0.41 | 0.80 | 15 | empty |
| 4 | 77 | 0.38 | 0.78 | 17 | empty |
| 5 | 60 | 0.32 | 0.75 | 18 | EDO |
Interfaces
1 interface between chains.
- A–D · 1576 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2WEL · Crystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in… · 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 A against A, TM-score 0.86
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
- Every structure of UniProt P62158
- Elsewhere: RCSB PDB 2WEL · PDBe 2WEL · UniProt Q13557 · UniProt P62158
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