Research workbench
Camp-dependent protein kinase a from cricetulus griseus in complex with fragment like molecule N-methyl-1-(5-pyridin-3-yloxyfuran-2-yl) methanamine
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
- 5N1D
- Type
- protein
- Length
- 369 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
- 8FZ
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 351 | 40% helix, 15% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor alpha-like protein | protein | 18 | 39% helix, 0% strand | A0A061IH64 |
Ligands and binding sites
- 8FZ · (5-pyridin-3-yloxyfuran-2-yl)methanamine · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
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 | 445 | 0.76 | 0.85 | 42 | 8FZ |
| 2 | 131 | 0.59 | 0.84 | 21 | MPD |
| 3 | 114 | 0.38 | 0.74 | 15 | empty |
| 4 | 72 | 0.31 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5N1D · 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 5N1D · PDBe 5N1D · UniProt P25321 · UniProt A0A061IH64
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