MolNFT v1 · #6040 · protein
Catalytic domain of human phosphodiesterase 4B2B
1F0J: “Catalytic domain of human phosphodiesterase 4B2B”. X-ray diffraction, 3 ligands (ARS, ZN, MG), 6 pockets (best druggability 0.79). MolNFT v1 #6040 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1F0J
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase 4B
- EC
- 3.1.4.17
- UniProt
- Q07343
- Ligands
- ARS, ZN, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase 4B (EC 3.1.4.17) | protein | 351 | 65% helix, 1% strand | Q07343 |
| B | Phosphodiesterase 4B (EC 3.1.4.17) | protein | 337 | 66% helix, 1% strand | Q07343 |
Ligands and binding sites
- ARS · Arsenic · metal · 5 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.79 | 0.91 | 44 | MG, ARS |
| 2 | 444 | 0.70 | 0.81 | 40 | MG, ARS |
| 3 | 455 | 0.58 | 0.74 | 46 | empty |
| 4 | 86 | 0.38 | 0.76 | 15 | ARS |
| 5 | 66 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 287 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 1F0J · PDBe 1F0J · UniProt Q07343
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