Research workbench
Crystal structure of (108-268)RIIB:C holoenzyme of camp-dependent protein kinase
Analyse Crystal structure of (108-268)RIIB:C holoenzyme of camp-dependent protein kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IDB
- Type
- protein
- Length
- 492 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 type…
- EC
- 2.7.11.11
- UniProt
- P05132, P12369
- Ligands
- ANP, MN
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 343 | 38% helix, 15% strand | P05132 |
| B | Camp-dependent protein kinase type II-beta regulatory subunit | protein | 149 | 28% helix, 32% strand | P12369 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.77 | 0.85 | 65 | MN, ANP |
| 2 | 161 | 0.46 | 0.76 | 22 | empty |
| 3 | 117 | 0.39 | 0.74 | 19 | empty |
| 4 | 74 | 0.36 | 0.76 | 17 | empty |
| 5 | 85 | 0.34 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1425 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3IDB · Crystal structure of (108-268)RIIb:C holoenzyme of cAMP-dependent protein kinase · the same entry in another collection · chain A against A, TM-score 1.00
- P12369 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase type II-beta… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P05132
- Every structure of UniProt P12369
- Elsewhere: RCSB PDB 3IDB · PDBe 3IDB · UniProt P05132 · UniProt P12369
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