Research workbench
The crystal structure of AMP-bound PDE4 suggests a mechanism for phosphodiesterase catalysis
Analyse The crystal structure of AMP-bound PDE4 suggests a mechanism for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PTW
- Type
- protein
- Length
- 1,322 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific phosphodiesterase PDE4D2
- EC
- 3.1.4.17
- UniProt
- Q08499
- Ligands
- AMP, ZN
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Camp-specific phosphodiesterase PDE4D2 (EC 3.1.4.17) | protein | 334 | 66% helix, 0% strand | Q08499 |
| B, C | Camp-specific phosphodiesterase PDE4D2 (EC 3.1.4.17) | protein | 327 | 66% helix, 1% strand | Q08499 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.88 | 0.89 | 128 | empty |
| 2 | 379 | 0.72 | 0.83 | 42 | ZN, AMP |
| 3 | 432 | 0.72 | 0.82 | 40 | ZN, AMP |
| 4 | 408 | 0.72 | 0.83 | 43 | ZN, AMP |
| 5 | 143 | 0.71 | 0.91 | 19 | empty |
Interfaces
6 interfaces between chains.
- B–D · 972 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 935 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 791 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 746 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 234 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1PTW · The Crystal Structure of AMP-Bound PDE4 Suggests a Mechanism for Phosphodiesterase… · 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 1PTW · PDBe 1PTW · UniProt Q08499
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