MolNFT v1 · #157026 · protein
Catalytic subunit of camp-dependent protein kinase a in complex with RYR2 K2879A, S2813D phosphomimetic (2699-2904) crystal form 1
6MM7 · 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), 12 pockets (best druggability…
- PDB
- 6MM7
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- 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
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 327 | 38% helix, 16% strand | P05132 |
| C, E | Ryanodine receptor 2 | protein | 206 | 53% helix, 5% strand | E9Q401 |
| D | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 324 | 39% helix, 16% strand | P05132 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, C, D
- CL · Chloride ion · ion · 2 copies · chains D, E
- FMT · Formic acid · additive · 8 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, D, E
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.77 | 0.81 | 71 | EDO |
| 2 | 913 | 0.76 | 0.79 | 69 | empty |
| 3 | 548 | 0.69 | 0.78 | 45 | ANP, EDO |
| 4 | 564 | 0.69 | 0.78 | 48 | ANP |
| 5 | 161 | 0.49 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1421 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1397 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 86 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6MM7 · Catalytic subunit of cAMP-dependent protein kinase A in complex with RyR2 K2879A, S2813D… · 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 P05132
- Every structure of UniProt E9Q401
- Elsewhere: RCSB PDB 6MM7 · PDBe 6MM7 · UniProt P05132 · UniProt E9Q401
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