Research workbench
Camp-dependent protein kinase a from cricetulus griseus in complex with fragment like molecule N-[3-(AMINOMETHYL)PHENYL]ACETAMIDE
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
- 5N3F
- Type
- protein
- Length
- 333 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
- Ligands
- 463
- Pockets
- 3 · best druggability 0.78
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 | 321 | 39% helix, 16% strand | P25321 |
| B | Camp dependent protein kinase inhibitor alpha-like protein | protein | 12 | 0% helix, 8% strand | — |
Ligands and binding sites
- 463 · N-[3-(aminomethyl)phenyl]acetamide · ligand · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.78 | 0.85 | 43 | 463 |
| 2 | 251 | 0.58 | 0.78 | 33 | MPD |
| 3 | 53 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 824 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 5N3F · 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
- Elsewhere: RCSB PDB 5N3F · PDBe 5N3F · UniProt P25321
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