Research workbench
Crystal structures of the catalytic domain of phosphodiesterase 4B2B complexed with AMP
Analyse Crystal structures of the catalytic domain of phosphodiesterase 4B2B complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ROR
- Type
- protein
- Length
- 675 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
- AMP, ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 338 | 65% helix, 0% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 337 | 65% helix, 1% strand | Q07343 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.71 | 0.81 | 47 | ZN, AMP |
| 2 | 450 | 0.70 | 0.81 | 38 | ZN, AMP |
| 3 | 425 | 0.58 | 0.75 | 48 | empty |
| 4 | 65 | 0.36 | 0.77 | 13 | empty |
| 5 | 73 | 0.35 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 319 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1ROR · Crystal structures of the catalytic domain of phosphodiesterase 4B2B complexed with AMP · 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 0.98
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 1ROR · PDBe 1ROR · UniProt Q07343
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