Research workbench
Target enzyme recognition by calmodulin: 2.4 ångströms structure of a calmodulin-peptide complex
Analyse Target enzyme recognition by calmodulin: 2.4 ångströms structure of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CDL
- Type
- protein
- Length
- 644 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; CALCIUM/CALMODULIN-dependent protein kinase type II alpha chain
- UniProt
- P62158, P11799
- Ligands
- CA
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Calmodulin | protein | 142 | 62% helix, 6% strand | P62158 |
| E, F | CALCIUM/CALMODULIN-dependent protein kinase type II alpha chain | protein | 19 | 84% helix, 0% strand | P11799 |
| G | CALCIUM/CALMODULIN-dependent protein kinase type II alpha chain | protein | 20 | 80% helix, 0% strand | P11799 |
| H | CALCIUM/CALMODULIN-dependent protein kinase type II alpha chain | protein | 18 | 89% helix, 0% strand | P11799 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.69 | 0.77 | 60 | empty |
| 2 | 100 | 0.58 | 0.86 | 34 | empty |
| 3 | 117 | 0.57 | 0.84 | 17 | empty |
| 4 | 207 | 0.53 | 0.78 | 35 | empty |
| 5 | 80 | 0.48 | 0.83 | 18 | empty |
Interfaces
12 interfaces between chains.
- B–F · 1485 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 1477 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 1437 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 1389 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 551 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1CDL · Target enzyme recognition by calmodulin: 2.4 ångströms structure of a calmodulin-peptide… · the same entry in another collection · chain B against B, TM-score 1.00
- P11799 · AlphaFold monomer V2.0 prediction for myosin light chain kinase, smooth muscle (P11799) · a predicted model of the same protein · chain H against A, TM-score 0.67
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 P62158
- Every structure of UniProt P11799
- Elsewhere: RCSB PDB 1CDL · PDBe 1CDL · UniProt P62158 · UniProt P11799
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