Research workbench
cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with fragment like molecule Thiophene-3-Carboximidamide
Analyse cAMP-dependent Protein Kinase A from Cricetulus griseus in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N3C
- Type
- protein
- Length
- 365 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.772
- Source
- Cricetulus griseus; SYNTHETIC CONSTRUCT
- Molecule
- cAMP-dependent protein kinase catalytic subunit alpha; cAMP dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P25321
- Ligands
- 8M2
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.772 · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 352 | 38% helix, 15% strand | P25321 |
| B | cAMP dependent protein kinase inhibitor alpha-like protein | protein | 13 | 0% helix, 8% strand | — |
Ligands and binding sites
- 8M2 · [azanyl(thiophen-3-yl)methylidene]azanium · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.82 | 0.91 | 42 | 8M2 |
| 2 | 260 | 0.58 | 0.78 | 39 | MPD |
| 3 | 61 | 0.33 | 0.76 | 15 | empty |
| 4 | 55 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5N3C · Camp-dependent protein kinase a from cricetulus griseus in complex with fragment like… · the same entry in another collection · chain A against A, TM-score 1.00
- P25321 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P25321
- Elsewhere: RCSB PDB 5N3C · PDBe 5N3C · UniProt P25321
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.