Research workbench
Crystal structure of cyclic nucleotide phosphodiesterase of APPR>P from arabidopsis thaliana
Analyse Crystal structure of cyclic nucleotide phosphodiesterase of APPR>P from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FSI
- Type
- protein
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic phosphodiesterase
- UniProt
- O04147
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclic phosphodiesterase | protein | 179 | 29% helix, 35% strand | O04147 |
| B | Cyclic phosphodiesterase | protein | 170 | 28% helix, 37% strand | O04147 |
| C | Cyclic phosphodiesterase | protein | 174 | 30% helix, 36% strand | O04147 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.87 | 0.88 | 113 | SO4 |
| 2 | 220 | 0.54 | 0.78 | 28 | SO4 |
| 3 | 184 | 0.53 | 0.78 | 24 | SO4 |
| 4 | 173 | 0.50 | 0.77 | 23 | SO4 |
| 5 | 77 | 0.34 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 423 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 423 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 357 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1FSI · Crystal structure of cyclic nucleotide phosphodiesterase of APPR>P from arabidopsis… · 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 B against A, TM-score 0.97
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 1FSI · PDBe 1FSI · UniProt O04147
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