Research workbench
Crystal structure of crosslink stabilized long-form PDE4B
Analyse Crystal structure of crosslink stabilized long-form PDE4B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WZI
- Type
- protein
- Length
- 836 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
- ZN, NA, MG, IOD
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53) | protein | 412 | 71% helix, 0% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.53) | protein | 424 | 71% helix, 1% strand | Q07343 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.82 | 0.91 | 53 | MG |
| 2 | 394 | 0.81 | 0.90 | 45 | MG |
| 3 | 89 | 0.54 | 0.85 | 17 | IOD |
| 4 | 131 | 0.54 | 0.82 | 24 | empty |
| 5 | 73 | 0.51 | 0.85 | 17 | IOD |
Interfaces
1 interface between chains.
- A–B · 4752 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4WZI · Crystal structure of crosslink stabilized long-form PDE4B · 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 4WZI · PDBe 4WZI · UniProt Q07343
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