MolNFT v1 · #127667 · protein
Camp-dependent protein kinase a from cricetulus griseus in complex with fragment like molecule 2-(2,3-DIHYDROBENZO[B][1,4]DIOXIN-6-yl) pyrrolidine
5N39 · Camp-dependent protein kinase catalytic subunit alpha: “Camp-dependent protein kinase a from cricetulus griseus in complex with fragment like molecule…”. X-ray diffraction, 1 ligand (8LZ), 2 pockets (best druggability 0.82). MolNFT…
- PDB
- 5N39
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P25321, A0A061IH64
- Ligands
- 8LZ
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 38% 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 | 351 | 39% helix, 15% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha-like protein | protein | 13 | 0% helix, 8% strand | A0A061IH64 |
Ligands and binding sites
- 8LZ · (2~{S})-2-(2,3-dihydro-1,4-benzodioxin-6-yl)pyrrolidin-1-ium · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.82 | 0.89 | 45 | 8LZ |
| 2 | 237 | 0.58 | 0.79 | 32 | MPD |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 5N39 · 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
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
- Every structure of UniProt A0A061IH64
- Elsewhere: RCSB PDB 5N39 · PDBe 5N39 · UniProt P25321 · UniProt A0A061IH64
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