Research workbench
Crystal structure of the human phosphodiesterase 9A catalytic domain complexed with ibmx
Analyse Crystal structure of the human phosphodiesterase 9A catalytic domain complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YY2
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A
- EC
- 3.1.4.35
- UniProt
- O76083
- Ligands
- IBM, ZN, MG
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 326 | 69% helix, 0% strand | O76083 |
| B | High-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9A (EC 3.1.4.35) | protein | 324 | 69% helix, 0% strand | O76083 |
Ligands and binding sites
- IBM · 3-isobutyl-1-methylxanthine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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 | 357 | 0.73 | 0.84 | 41 | ZN, MG, IBM |
| 2 | 318 | 0.71 | 0.85 | 41 | MG, IBM |
| 3 | 111 | 0.38 | 0.75 | 22 | empty |
| 4 | 60 | 0.36 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 871 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2YY2 · Crystal structure of the human Phosphodiesterase 9A catalytic domain complexed with IBMX · 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 B 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 O76083
- Elsewhere: RCSB PDB 2YY2 · PDBe 2YY2 · UniProt O76083
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