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Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state
Analyse Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BG2
- Type
- protein
- Length
- 1,325 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.83
- Source
- Homo sapiens
- Molecule
- cGMP-dependent protein kinase 1
- EC
- 2.7.11.12
- UniProt
- Q13976
- Ligands
- ANP, MN
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · resolution 1.83 · 4 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | cGMP-dependent protein kinase 1 (EC 2.7.11.12) | protein | 335 | 39% helix, 16% strand | Q13976 |
| B | cGMP-dependent protein kinase 1 (EC 2.7.11.12) | protein | 326 | 37% helix, 17% strand | Q13976 |
| A | cGMP-dependent protein kinase 1 (EC 2.7.11.12) | protein | 336 | 39% helix, 17% strand | Q13976 |
| D | cGMP-dependent protein kinase 1 (EC 2.7.11.12) | protein | 328 | 37% helix, 16% strand | Q13976 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains C, B, A, D
- MN · Manganese (II) ion · metal · 8 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.73 | 0.87 | 37 | ANP, MN |
| 2 | 228 | 0.71 | 0.86 | 35 | ANP, MN |
| 3 | 432 | 0.71 | 0.81 | 61 | ANP, MN |
| 4 | 670 | 0.70 | 0.78 | 91 | empty |
| 5 | 377 | 0.66 | 0.79 | 40 | ANP, MN |
Interfaces
4 interfaces between chains.
- C–A · 616 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 415 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 207 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 144 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6BG2 · Crystal structure of cgmp-dependent protein kinase ialpha (pkg ialpha) catalytic domain… · the same entry in another collection · chain D against D, TM-score 1.00
- Q13976 · AlphaFold monomer V2.0 prediction for cgmp-dependent protein kinase 1 (Q13976) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q13976
- Elsewhere: RCSB PDB 6BG2 · PDBe 6BG2 · UniProt Q13976
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