Research workbench
Structure and allostery of the PKA riib tetrameric holoenzyme
Analyse Structure and allostery of the PKA riib tetrameric holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TNQ
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase, camp-dependent, catalytic, alpha; Camp-dependent protein kinase type…
- UniProt
- A1L1M0, P31324
- Ligands
- ADP, MG
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Protein kinase, camp-dependent, catalytic, alpha | protein | 334 | 36% helix, 14% strand | A1L1M0 |
| A | Camp-dependent protein kinase type II-beta regulatory subunit | protein | 270 | 26% helix, 31% strand | P31324 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.74 | 0.83 | 59 | MG, ADP |
| 2 | 367 | 0.62 | 0.78 | 43 | empty |
| 3 | 213 | 0.54 | 0.78 | 32 | empty |
| 4 | 73 | 0.43 | 0.81 | 18 | empty |
| 5 | 127 | 0.40 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 1964 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3TNQ · Structure and Allostery of the PKA RIIb Tetrameric Holoenzyme · the same entry in another collection · chain B against B, TM-score 1.00
- P31324 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase type II-beta… · a predicted model of the same protein · chain A against A, TM-score 0.87
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 A1L1M0
- Every structure of UniProt P31324
- Elsewhere: RCSB PDB 3TNQ · PDBe 3TNQ · UniProt A1L1M0 · UniProt P31324
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