Research workbench
Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 phosphorylation domain (2699-2904)
Analyse Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MM6
- Type
- protein
- Length
- 1,041 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.39
- Source
- Mus musculus
- Molecule
- cAMP-dependent protein kinase catalytic subunit alpha; Ryanodine receptor 2
- EC
- 2.7.11.11
- UniProt
- P05132, E9Q401
- Ligands
- ANP, CL
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.39 · 4 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 322 | 38% helix, 17% strand | P05132 |
| E | cAMP-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 320 | 38% helix, 17% strand | P05132 |
| F | Ryanodine receptor 2 | protein | 198 | 50% helix, 7% strand | E9Q401 |
| D | Ryanodine receptor 2 | protein | 201 | 48% helix, 7% strand | E9Q401 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains C, D, E
- CL · Chloride ion · ion · 3 copies · chains C, D, E, F
- ACT · Acetate ion · additive · chains C, D
- PGE · Triethylene glycol · additive · chains C
- EDO · 1,2-ethanediol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.76 | 0.83 | 64 | empty |
| 2 | 938 | 0.72 | 0.76 | 59 | ACT |
| 3 | 838 | 0.70 | 0.75 | 64 | empty |
| 4 | 544 | 0.69 | 0.79 | 45 | ANP, EDO |
| 5 | 513 | 0.67 | 0.78 | 45 | ANP |
Interfaces
3 interfaces between chains.
- E–F · 1534 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 25 hydrogen bonds · protein-protein
- C–E · 480 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6MM6 · Catalytic subunit of camp-dependent protein kinase a in complex with RYR2 phosphorylation… · the same entry in another collection · chain C against C, TM-score 1.00
- P05132 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase catalytic subunit… · a predicted model of the same protein · chain E against A, TM-score 0.93
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 E9Q401
- Elsewhere: RCSB PDB 6MM6 · PDBe 6MM6 · UniProt P05132 · UniProt E9Q401
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