Research workbench
Crystal structure of human phosphodiesterase 4B with regulatory domain and D155988
Analyse Crystal structure of human phosphodiesterase 4B with regulatory domain and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G45
- Type
- protein
- Length
- 741 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
- 988, ZN, MG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 371 | 67% helix, 1% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 370 | 67% helix, 1% strand | Q07343 |
Ligands and binding sites
- 988 · 8-(3-nitrophenyl)-6-(pyridin-4-ylmethyl)quinoline · 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.84 | 0.85 | 87 | empty |
| 2 | 417 | 0.82 | 0.90 | 55 | MG, 988 |
| 3 | 476 | 0.82 | 0.89 | 60 | MG, 988 |
| 4 | 101 | 0.49 | 0.81 | 13 | empty |
| 5 | 74 | 0.46 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1109 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3G45 · Crystal structure of human phosphodiesterase 4b with regulatory domain and d155988 · 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 B against A, TM-score 0.90
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 3G45 · PDBe 3G45 · UniProt Q07343
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