Research workbench
Neutron diffraction reveals hydrogen bonds critical for cGMP-selective activation: Insights for PKG agonist design
Analyse Neutron diffraction reveals hydrogen bonds critical for cGMP-selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QX5
- Type
- protein
- Length
- 127 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.318
- Source
- Homo sapiens
- Molecule
- cGMP-dependent protein kinase 1
- EC
- 2.7.11.12
- UniProt
- Q13976
- Ligands
- CMP, IOD
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · resolution 1.318 · 1 distinct chain · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | cGMP-dependent protein kinase 1 (EC 2.7.11.12) | protein | 127 | 28% helix, 32% strand | Q13976 |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · chains A
- IOD · Iodide ion · ion · 18 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.55 | 0.83 | 22 | CMP, IOD |
Compared structures
- 4QX5 · Neutron diffraction reveals hydrogen bonds critical for cgmp-selective activation… · the same entry in another collection · chain A against A, 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 0.91
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 4QX5 · PDBe 4QX5 · UniProt Q13976
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