Research workbench
human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cGMP
Analyse human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DYQ
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens
- Molecule
- High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
- EC
- 3.1.4.35
- UniProt
- O76083
- Ligands
- PCG, IBM, NA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.5 · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 328 | 70% helix, 0% strand | O76083 |
Ligands and binding sites
- PCG · Cyclic guanosine monophosphate · ligand · chains A
- IBM · 3-isobutyl-1-methylxanthine · ligand · chains B
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.74 | 0.85 | 46 | NA, PCG |
| 2 | 334 | 0.72 | 0.84 | 41 | NA, IBM |
| 3 | 80 | 0.42 | 0.80 | 15 | empty |
| 4 | 107 | 0.37 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3DYQ · Human phosphodiestrase 9 (inhibited by omitting divalent cation) in complex with cgmp · the same entry in another collection · chain A against A, TM-score 1.00
- O76083 · AlphaFold monomer V2.0 prediction for high affinity cgmp-specific 3',5'-cyclic… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O76083
- Elsewhere: RCSB PDB 3DYQ · PDBe 3DYQ · UniProt O76083
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