MolNFT v1 · #128536 · protein
Crystal structure of the protein-kinase a catalytic subunit from criteculus griseus in complex with compound RKP032
5NTJ · Camp-dependent protein kinase catalytic subunit alpha: “Crystal structure of the protein-kinase a catalytic subunit from criteculus griseus in complex with compound…”. X-ray diffraction, 1 ligand (RIP), 3 pockets (best druggability…
- PDB
- 5NTJ
- Type
- protein
- Length
- 368 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
- RIP
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% 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 | 350 | 39% helix, 15% strand | P25321 |
| B | Camp-dependent protein kinase inhibitor | protein | 18 | 39% helix, 0% strand | A0A061IH64 |
Ligands and binding sites
- RIP · beta-D-ribopyranose · ligand · chains A, B
- 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
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 | 710 | 0.70 | 0.77 | 49 | empty |
| 2 | 256 | 0.59 | 0.79 | 32 | MPD |
| 3 | 64 | 0.28 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 746 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent (phosphorylation, covalent ligand).
Compared structures
- 5NTJ · Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in… · 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 5NTJ · PDBe 5NTJ · UniProt P25321 · UniProt A0A061IH64
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