Research workbench
Crystal structure of PDE4D catalytic domain complexed with 17
Analyse Crystal structure of PDE4D catalytic domain complexed with 17 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W4X
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499
- Ligands
- 8G7, ZN, MG
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 324 | 67% helix, 1% strand | Q08499 |
Ligands and binding sites
- 8G7 · (2R,4S)-2-(2-hydroxyethyl)-2,6-dimethyl-4-(2-methylprop-1-enyl)-3,4-dihydropyrano[3,2-C][1, 8]naphthyridin-5-one · 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.73 | 0.83 | 41 | MG, 8G7 |
| 2 | 430 | 0.71 | 0.82 | 46 | MG, 8G7 |
| 3 | 187 | 0.58 | 0.81 | 22 | empty |
| 4 | 191 | 0.51 | 0.77 | 25 | empty |
| 5 | 68 | 0.36 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 831 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7W4X · Crystal structure of PDE4D catalytic domain complexed with 17 · the same entry in another collection · 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 Q08499
- Elsewhere: RCSB PDB 7W4X · PDBe 7W4X · UniProt Q08499
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.