MolNFT v1 · #109358 · protein
Crystal structure of crosslink stabilized long-form PDE4B in complex with (R)-(-)-rolipram
4X0F · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Crystal structure of crosslink stabilized long-form PDE4B in complex with (R)-(-)-rolipram”. X-ray diffraction, 4 ligands (ROL, ZN, MG), 8 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4X0F
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4B
- EC
- 3.1.4.53
- UniProt
- Q07343
- Ligands
- ROL, ZN, MG, IOD
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53) | protein | 411 | 67% helix, 0% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53) | protein | 414 | 69% helix, 0% strand | Q07343 |
Ligands and binding sites
- ROL · Rolipram · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.83 | 0.84 | 113 | IOD, ROL, MG |
| 2 | 472 | 0.83 | 0.90 | 53 | ROL |
| 3 | 219 | 0.57 | 0.79 | 32 | empty |
| 4 | 122 | 0.55 | 0.83 | 18 | IOD |
| 5 | 87 | 0.44 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4420 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4X0F · Crystal structure of crosslink stabilized long-form PDE4B in complex with (R)-(-)-rolipram · the same entry in another collection · chain A against A, TM-score 1.00
- Q07343 · AlphaFold monomer V2.0 prediction for camp-specific 3',5'-cyclic phosphodiesterase 4B… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q07343
- Elsewhere: RCSB PDB 4X0F · PDBe 4X0F · UniProt Q07343
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