Research workbench
Crystal structure of the D/D domain of PKA from S. cerevisiae
Analyse Crystal structure of the D/D domain of PKA from S. cerevisiae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XQK
- Type
- protein
- Length
- 355 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.56
- Source
- Saccharomyces cerevisiae
- Molecule
- cAMP-dependent protein kinase regulatory subunit
- UniProt
- P07278
- Ligands
- CL
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.56 · 8 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cAMP-dependent protein kinase regulatory subunit | protein | 47 | 81% helix, 0% strand | P07278 |
| B | cAMP-dependent protein kinase regulatory subunit | protein | 43 | 86% helix, 0% strand | P07278 |
| C | cAMP-dependent protein kinase regulatory subunit | protein | 41 | 85% helix, 0% strand | P07278 |
| D | cAMP-dependent protein kinase regulatory subunit | protein | 44 | 86% helix, 0% strand | P07278 |
| E | cAMP-dependent protein kinase regulatory subunit | protein | 45 | 82% helix, 0% strand | P07278 |
| F | cAMP-dependent protein kinase regulatory subunit | protein | 46 | 83% helix, 0% strand | P07278 |
| G | cAMP-dependent protein kinase regulatory subunit | protein | 45 | 82% helix, 0% strand | P07278 |
| H | cAMP-dependent protein kinase regulatory subunit | protein | 44 | 84% helix, 0% strand | P07278 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.64 | 0.78 | 40 | empty |
| 2 | 71 | 0.63 | 0.91 | 23 | empty |
| 3 | 296 | 0.55 | 0.76 | 28 | empty |
Interfaces
15 interfaces between chains.
- E–F · 947 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 929 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 831 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 628 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6XQK · Crystal structure of the D/D domain of PKA from S. cerevisiae · the same entry in another collection · chain H against H, TM-score 1.00
- P07278 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase regulatory subunit… · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P07278
- Elsewhere: RCSB PDB 6XQK · PDBe 6XQK · UniProt P07278
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