Research workbench
The structure of CA2+ sensor (case-12)
Analyse The structure of CA2+ sensor (case-12) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O78
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin light chain kinase, smooth MUSCLE,GREEN fluorescent PROTEIN,GREEN fluorescent…
- EC
- 2.7.11.18
- UniProt
- P11799, P42212, P0DP23
- Ligands
- CR2, CA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin light chain kinase, smooth MUSCLE,GREEN fluorescent PROTEIN,GREEN fluorescent PROTEIN,CALMODULIN-1 (EC 2.7.11.18) | protein | 402 | 32% helix, 30% strand | P11799, P42212, P0DP23 |
| B | Myosin light chain kinase, smooth MUSCLE,GREEN fluorescent PROTEIN,GREEN fluorescent PROTEIN,CALMODULIN-1 (EC 2.7.11.18) | protein | 400 | 32% helix, 30% strand | P11799, P42212, P0DP23 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.78 | 0.85 | 56 | CR2 |
| 2 | 399 | 0.75 | 0.85 | 47 | CR2 |
| 3 | 186 | 0.62 | 0.83 | 34 | empty |
| 4 | 189 | 0.58 | 0.81 | 26 | empty |
| 5 | 101 | 0.53 | 0.83 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 3917 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 3O78 · The structure of Ca2+ Sensor (Case-12) · the same entry in another collection · chain A against A, TM-score 1.00
- P42212 · AlphaFold monomer V2.0 prediction for green fluorescent protein (P42212) · a predicted model of the same protein · chain A against A, TM-score 0.37
- P11799 · AlphaFold monomer V2.0 prediction for myosin light chain kinase, smooth muscle (P11799) · a predicted model of the same protein · chain A against A, TM-score 0.28
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain A against A, TM-score 0.20
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 P11799
- Every structure of UniProt P42212
- Every structure of UniProt P0DP23
- Elsewhere: RCSB PDB 3O78 · PDBe 3O78 · UniProt P11799 · UniProt P42212 · UniProt P0DP23
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