Research workbench
Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with BPN5004
Analyse Crystal structure of the PDE4D catalytic domain and UCR2 regulatory helix with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BOJ
- Type
- protein
- Length
- 1,343 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-specific 3',5'-cyclic phosphodiesterase 4D
- EC
- 3.1.4.53
- UniProt
- Q08499, Q07343
- Ligands
- E31, ZN, MG, CL
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 335 | 67% helix, 1% strand | Q08499, Q07343 |
| C | Camp-specific 3',5'-cyclic phosphodiesterase 4D (EC 3.1.4.53) | protein | 338 | 67% helix, 1% strand | Q08499, Q07343 |
Ligands and binding sites
- E31 · 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, C, B, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.84 | 0.93 | 52 | MG, E31 |
| 2 | 331 | 0.82 | 0.92 | 49 | MG, E31 |
| 3 | 921 | 0.81 | 0.83 | 91 | MPD |
| 4 | 416 | 0.81 | 0.89 | 58 | MG, E31 |
| 5 | 528 | 0.81 | 0.87 | 60 | empty |
Interfaces
5 interfaces between chains.
- C–D · 790 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 773 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 727 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 686 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 178 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6BOJ · Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q08499
- Every structure of UniProt Q07343
- Elsewhere: RCSB PDB 6BOJ · PDBe 6BOJ · UniProt Q08499 · UniProt Q07343
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