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Catalytic domain of human phosphodiesterase 4B in complex with (R)- mesopram
Analyse Catalytic domain of human phosphodiesterase 4B in complex with (R)- mesopram in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XM6
- Type
- protein
- Length
- 672 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
- 5RM, ZN, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 68% 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 | 338 | 69% helix, 1% strand | Q07343 |
| B | Camp-specific 3',5'-cyclic phosphodiesterase 4B (EC 3.1.4.17) | protein | 334 | 68% helix, 1% strand | Q07343 |
Ligands and binding sites
- 5RM · (5R)-5-(4-methoxy-3-propoxyphenyl)-5-methyl-1,3-oxazolidin-2-one · 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.80 | 0.83 | 93 | MG, 5RM |
| 2 | 330 | 0.80 | 0.90 | 44 | MG, 5RM |
| 3 | 127 | 0.51 | 0.81 | 22 | empty |
| 4 | 75 | 0.29 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 866 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 1XM6 · Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Mesopram · 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 0.96
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 1XM6 · PDBe 1XM6 · UniProt Q07343
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