MolNFT v1 · #147734 · protein
Crystal structure of the protein-kinase a catalytic subunit from criteculus griseus in complex with compounds RKP120 and ADP
6EM7 · Camp-dependent protein kinase catalytic subunit alpha: “Crystal structure of the protein-kinase a catalytic subunit from criteculus griseus in complex with compounds…”. X-ray diffraction, 2 ligands (ADP, RIP), 5 pockets (best…
- PDB
- 6EM7
- Type
- protein
- Length
- 359 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; UPF0418 protein FAM164A
- EC
- 2.7.11.11
- UniProt
- P25321, G3HK48
- Ligands
- ADP, RIP
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 341 | 39% helix, 15% strand | P25321 |
| D | UPF0418 protein FAM164A | protein | 18 | 33% helix, 0% strand | G3HK48 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A, D
- RIP · beta-D-ribopyranose · ligand · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
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 | 218 | 0.81 | 0.94 | 42 | ADP |
| 2 | 78 | 0.46 | 0.81 | 13 | MPD |
| 3 | 89 | 0.32 | 0.73 | 17 | empty |
| 4 | 58 | 0.30 | 0.75 | 13 | empty |
| 5 | 60 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–D · 933 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent (phosphorylation, covalent ligand).
Compared structures
- 6EM7 · Crystal Structure of the Protein-Kinase A catalytic subunit from Criteculus Griseus in… · 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 P25321
- Every structure of UniProt G3HK48
- Elsewhere: RCSB PDB 6EM7 · PDBe 6EM7 · UniProt P25321 · UniProt G3HK48
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