MolNFT v1 · #157027 · protein
Catalytic subunit of camp-dependent protein kinase a in complex with RYR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 2
6MM8 · Camp-dependent protein kinase catalytic subunit alpha: “Catalytic subunit of camp-dependent protein kinase a in complex with RYR2 K2879A, S2813D phosphomimetic…”. X-ray diffraction, 2 ligands (ANP, CL), 7 pockets (best druggability…
- PDB
- 6MM8
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Ryanodine receptor 2
- EC
- 2.7.11.11
- UniProt
- P05132, E9Q401
- Ligands
- ANP, CL
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 326 | 39% helix, 16% strand | P05132 |
| D | Ryanodine receptor 2 | protein | 206 | 54% helix, 5% strand | E9Q401 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains C, D
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 5 copies · chains C, D
- ACY · Acetic acid · additive · 2 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.79 | 0.82 | 51 | empty |
| 2 | 567 | 0.69 | 0.78 | 47 | ANP, EDO |
| 3 | 158 | 0.48 | 0.77 | 28 | empty |
| 4 | 141 | 0.43 | 0.75 | 15 | EDO |
| 5 | 105 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- C–D · 1408 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6MM8 · Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D… · the same entry in another collection · chain C against C, 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 P05132
- Every structure of UniProt E9Q401
- Elsewhere: RCSB PDB 6MM8 · PDBe 6MM8 · UniProt P05132 · UniProt E9Q401
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