Research workbench
Semi-reduced cyclic nucleotide phosphodiesterase from arabidopsis thaliana
Analyse Semi-reduced cyclic nucleotide phosphodiesterase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JH6
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- O04147
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclic phosphodiesterase (EC 3.1.4.-) | protein | 181 | 30% helix, 35% strand | O04147 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.76 | 0.78 | 67 | SO4 |
| 2 | 81 | 0.38 | 0.77 | 14 | empty |
| 3 | 77 | 0.37 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1JH6 · Semi-reduced Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- O04147 · AlphaFold monomer V2.0 prediction for cyclic phosphodiesterase (O04147) · 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 O04147
- Elsewhere: RCSB PDB 1JH6 · PDBe 1JH6 · UniProt O04147
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