Research workbench
The structure of PDE4A with pentoxifylline at 2.84A resolution
Analyse The structure of PDE4A with pentoxifylline at 2.84A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TVX
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4A
- EC
- 3.1.4.17
- UniProt
- P27815
- Ligands
- PNX, ZN, MG, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Camp-specific 3',5'-cyclic phosphodiesterase 4A (EC 3.1.4.17) | protein | 334 | 66% helix, 1% strand | P27815 |
Ligands and binding sites
- PNX · 3,7-dimethyl-1-(5-oxohexyl)-3,7-dihydro-1H-purine-2,6-dione · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.79 | 0.81 | 99 | empty |
| 2 | 459 | 0.73 | 0.82 | 42 | MG, PNX |
| 3 | 441 | 0.72 | 0.82 | 44 | MG, PNX |
| 4 | 68 | 0.37 | 0.78 | 16 | empty |
| 5 | 68 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3TVX · The structure of PDE4A with pentoxifylline at 2.84A resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P27815 · AlphaFold monomer V2.0 prediction for camp-specific 3',5'-cyclic phosphodiesterase 4A… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P27815
- Elsewhere: RCSB PDB 3TVX · PDBe 3TVX · UniProt P27815
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