MolNFT v1 · #27550 · protein
Catalytic domain of human phosphodiesterase 4B in complex with (R,S)- rolipram
1XN0 · Camp-specific 3',5'-cyclic phosphodiesterase 4B: “Catalytic domain of human phosphodiesterase 4B in complex with (R,S)- rolipram”. X-ray diffraction, 3 ligands (ROL, ZN, MG), 7 pockets (best druggability 0.73). MolNFT v1 #27550 on…
- PDB
- 1XN0
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4B
- EC
- 3.1.4.17
- UniProt
- Q07343
- Ligands
- ROL, ZN, MG
- Pockets
- 7 · best druggability 0.73
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 4B (EC 3.1.4.17) | protein | 323 | 66% helix, 1% strand | Q07343 |
Ligands and binding sites
- ROL · Rolipram · ligand · 4 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.73 | 0.84 | 39 | MG, ROL |
| 2 | 383 | 0.71 | 0.83 | 44 | MG, ROL |
| 3 | 183 | 0.59 | 0.81 | 21 | empty |
| 4 | 157 | 0.52 | 0.79 | 21 | empty |
| 5 | 196 | 0.46 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 865 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 1XN0 · Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R,S)-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 1XN0 · PDBe 1XN0 · UniProt Q07343
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